HW6.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 1. Сборка длинных ридов"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Для запуска Canu посмотрим на размер генома:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Genome size: 4639675\n"
     ]
    }
   ],
   "source": [
    "ref_len = 0\n",
    "f = open('./homework6/reference.fasta', 'r')\n",
    "for line in f:\n",
    "    if line.startswith('>'):\n",
    "        pass\n",
    "    else:\n",
    "        line = line.strip()\n",
    "        ref_len += len(line)\n",
    "print(f'Genome size: {ref_len}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "! /Users/olga/miniconda3/pkgs/canu-1.5-pl5.22.0_1/bin/canu -p pacbio10 -d pacbio10 genomesize=4.7m -pacbio-raw ./homework6/pacbio_10x.fq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/miniconda3/pkgs/canu-1.5-pl5.22.0_1/bin/canu -p pacbio20 -d pacbio20 genomesize=4.7m -pacbio-raw ./homework6/pacbio_20x.fq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/miniconda3/pkgs/canu-1.5-pl5.22.0_1/bin/canu -p pacbio40 -d pacbio40 genomesize=4.7m -pacbio-raw ./homework6/pacbio_40x.fq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/miniconda3/pkgs/canu-1.5-pl5.22.0_1/bin/canu -p pacbio80 -d pacbio80 genomesize=4.7m -pacbio-raw ./homework6/pacbio_80x.fq"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 2. Сборка коротких ридов"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Собираем с помощью Spades"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/Downloads/SPAdes-3.15.2/bin/spades.py -1 ./homework6/illumina.100x.1.fq -2 ./homework6/illumina.100x.2.fq -o illumina"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 3. Гибридная сборка"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Собираем с помощью Spades"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/Downloads/SPAdes-3.15.2/bin/spades.py -1 ./homework6/illumina.100x.1.fq -2 ./homework6/illumina.100x.2.fq --pacbio ./homework6/pacbio_10x.fq -o illumina_pacbio10"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/Downloads/SPAdes-3.15.2/bin/spades.py -1 ./homework6/illumina.100x.1.fq -2 ./homework6/illumina.100x.2.fq --pacbio ./homework6/pacbio_20x.fq -o illumina_pacbio20"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/Downloads/SPAdes-3.15.2/bin/spades.py -1 ./homework6/illumina.100x.1.fq -2 ./homework6/illumina.100x.2.fq --pacbio ./homework6/pacbio_40x.fq -o illumina_pacbio40"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/Downloads/SPAdes-3.15.2/bin/spades.py -1 ./homework6/illumina.100x.1.fq -2 ./homework6/illumina.100x.2.fq --pacbio ./homework6/pacbio_80x.fq -o illumina_pacbio80"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 4. Сравним сборки с помощью quast"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "! /Users/olga/Downloads/quast-5.0.2/quast.py \\\n",
    "pacbio10/pacbio10.contigs.fasta \\\n",
    "pacbio20/pacbio20.contigs.fasta \\\n",
    "pacbio40/pacbio40.contigs.fasta \\\n",
    "pacbio80/pacbio80.contigs.fasta \\\n",
    "illumina/contigs.fasta \\\n",
    "illumina_pacbio10/contigs.fasta \\\n",
    "illumina_pacbio20/contigs.fasta \\\n",
    "illumina_pacbio40/contigs.fasta \\\n",
    "illumina_pacbio80/contigs.fasta \\\n",
    "-R homework6/reference.fasta \\\n",
    "-o quast_result"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 5. Проанализируем результаты (на основе отчёта, сгенерированного quast)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
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       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
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       "        text-align: right;\n",
       "    }\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Assembly</th>\n",
       "      <th>pacbio10.contigs</th>\n",
       "      <th>pacbio20.contigs</th>\n",
       "      <th>pacbio40.contigs</th>\n",
       "      <th>pacbio80.contigs</th>\n",
       "      <th>illumina_contigs</th>\n",
       "      <th>illumina_pacbio10_contigs</th>\n",
       "      <th>illumina_pacbio20_contigs</th>\n",
       "      <th>illumina_pacbio40_contigs</th>\n",
       "      <th>illumina_pacbio80_contigs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td># contigs (&gt;= 0 bp)</td>\n",
       "      <td>94</td>\n",
       "      <td>22</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>167</td>\n",
       "      <td>145</td>\n",
       "      <td>140</td>\n",
       "      <td>135</td>\n",
       "      <td>136</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td># contigs (&gt;= 1000 bp)</td>\n",
       "      <td>94</td>\n",
       "      <td>22</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>87</td>\n",
       "      <td>63</td>\n",
       "      <td>62</td>\n",
       "      <td>59</td>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td># contigs (&gt;= 5000 bp)</td>\n",
       "      <td>92</td>\n",
       "      <td>22</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>62</td>\n",
       "      <td>46</td>\n",
       "      <td>47</td>\n",
       "      <td>44</td>\n",
       "      <td>44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td># contigs (&gt;= 10000 bp)</td>\n",
       "      <td>89</td>\n",
       "      <td>21</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>57</td>\n",
       "      <td>45</td>\n",
       "      <td>46</td>\n",
       "      <td>44</td>\n",
       "      <td>44</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td># contigs (&gt;= 25000 bp)</td>\n",
       "      <td>55</td>\n",
       "      <td>20</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>47</td>\n",
       "      <td>39</td>\n",
       "      <td>39</td>\n",
       "      <td>38</td>\n",
       "      <td>37</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td># contigs (&gt;= 50000 bp)</td>\n",
       "      <td>24</td>\n",
       "      <td>18</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>31</td>\n",
       "      <td>29</td>\n",
       "      <td>30</td>\n",
       "      <td>30</td>\n",
       "      <td>29</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Total length (&gt;= 0 bp)</td>\n",
       "      <td>3540004</td>\n",
       "      <td>4598820</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>4567161</td>\n",
       "      <td>4580922</td>\n",
       "      <td>4581204</td>\n",
       "      <td>4581146</td>\n",
       "      <td>4582009</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Total length (&gt;= 1000 bp)</td>\n",
       "      <td>3540004</td>\n",
       "      <td>4598820</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>4548539</td>\n",
       "      <td>4564350</td>\n",
       "      <td>4566832</td>\n",
       "      <td>4567604</td>\n",
       "      <td>4568712</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Total length (&gt;= 5000 bp)</td>\n",
       "      <td>3530802</td>\n",
       "      <td>4598820</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>4493976</td>\n",
       "      <td>4526103</td>\n",
       "      <td>4538061</td>\n",
       "      <td>4538834</td>\n",
       "      <td>4537248</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Total length (&gt;= 10000 bp)</td>\n",
       "      <td>3506582</td>\n",
       "      <td>4591727</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>4458325</td>\n",
       "      <td>4518046</td>\n",
       "      <td>4529247</td>\n",
       "      <td>4538834</td>\n",
       "      <td>4537248</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Total length (&gt;= 25000 bp)</td>\n",
       "      <td>2917321</td>\n",
       "      <td>4575443</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>4312386</td>\n",
       "      <td>4439862</td>\n",
       "      <td>4434562</td>\n",
       "      <td>4460648</td>\n",
       "      <td>4442027</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Total length (&gt;= 50000 bp)</td>\n",
       "      <td>1757051</td>\n",
       "      <td>4506249</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>3762852</td>\n",
       "      <td>4111348</td>\n",
       "      <td>4140604</td>\n",
       "      <td>4182994</td>\n",
       "      <td>4168651</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td># contigs</td>\n",
       "      <td>94</td>\n",
       "      <td>22</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>97</td>\n",
       "      <td>70</td>\n",
       "      <td>66</td>\n",
       "      <td>63</td>\n",
       "      <td>64</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Largest contig</td>\n",
       "      <td>176275</td>\n",
       "      <td>751732</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>221601</td>\n",
       "      <td>349819</td>\n",
       "      <td>349819</td>\n",
       "      <td>349819</td>\n",
       "      <td>349819</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Total length</td>\n",
       "      <td>3540004</td>\n",
       "      <td>4598820</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>4555330</td>\n",
       "      <td>4568726</td>\n",
       "      <td>4569348</td>\n",
       "      <td>4570120</td>\n",
       "      <td>4571228</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Reference length</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "      <td>4639675</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>GC (%)</td>\n",
       "      <td>50.40</td>\n",
       "      <td>50.76</td>\n",
       "      <td>50.78</td>\n",
       "      <td>50.80</td>\n",
       "      <td>50.74</td>\n",
       "      <td>50.76</td>\n",
       "      <td>50.76</td>\n",
       "      <td>50.76</td>\n",
       "      <td>50.76</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Reference GC (%)</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "      <td>50.79</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>N50</td>\n",
       "      <td>49862</td>\n",
       "      <td>273171</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>129054</td>\n",
       "      <td>154542</td>\n",
       "      <td>154542</td>\n",
       "      <td>154542</td>\n",
       "      <td>154542</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>NG50</td>\n",
       "      <td>41894</td>\n",
       "      <td>273171</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>129054</td>\n",
       "      <td>154542</td>\n",
       "      <td>152878</td>\n",
       "      <td>152878</td>\n",
       "      <td>154542</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>N75</td>\n",
       "      <td>30852</td>\n",
       "      <td>199323</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>60768</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>NG75</td>\n",
       "      <td>10787</td>\n",
       "      <td>199323</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>59669</td>\n",
       "      <td>95450</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>L50</td>\n",
       "      <td>25</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>14</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>LG50</td>\n",
       "      <td>37</td>\n",
       "      <td>5</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>14</td>\n",
       "      <td>11</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>L75</td>\n",
       "      <td>46</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>26</td>\n",
       "      <td>20</td>\n",
       "      <td>21</td>\n",
       "      <td>21</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>LG75</td>\n",
       "      <td>87</td>\n",
       "      <td>10</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>27</td>\n",
       "      <td>21</td>\n",
       "      <td>21</td>\n",
       "      <td>21</td>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td># misassemblies</td>\n",
       "      <td>10</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td># misassembled contigs</td>\n",
       "      <td>6</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>Misassembled contigs length</td>\n",
       "      <td>357608</td>\n",
       "      <td>1189535</td>\n",
       "      <td>4641141</td>\n",
       "      <td>4649321</td>\n",
       "      <td>0</td>\n",
       "      <td>808786</td>\n",
       "      <td>349819</td>\n",
       "      <td>349819</td>\n",
       "      <td>855583</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td># local misassemblies</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>5</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td># scaffold gap ext. mis.</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td># scaffold gap loc. mis.</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td># unaligned mis. contigs</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td># unaligned contigs</td>\n",
       "      <td>0 + 0 part</td>\n",
       "      <td>0 + 0 part</td>\n",
       "      <td>0 + 0 part</td>\n",
       "      <td>0 + 0 part</td>\n",
       "      <td>1 + 0 part</td>\n",
       "      <td>1 + 0 part</td>\n",
       "      <td>1 + 0 part</td>\n",
       "      <td>1 + 0 part</td>\n",
       "      <td>1 + 0 part</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>Unaligned length</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>542</td>\n",
       "      <td>542</td>\n",
       "      <td>542</td>\n",
       "      <td>542</td>\n",
       "      <td>542</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>Genome fraction (%)</td>\n",
       "      <td>76.336</td>\n",
       "      <td>98.850</td>\n",
       "      <td>99.995</td>\n",
       "      <td>99.998</td>\n",
       "      <td>98.142</td>\n",
       "      <td>98.439</td>\n",
       "      <td>98.457</td>\n",
       "      <td>98.476</td>\n",
       "      <td>98.499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>Duplication ratio</td>\n",
       "      <td>1.000</td>\n",
       "      <td>1.003</td>\n",
       "      <td>1.000</td>\n",
       "      <td>1.002</td>\n",
       "      <td>1.000</td>\n",
       "      <td>1.000</td>\n",
       "      <td>1.000</td>\n",
       "      <td>1.000</td>\n",
       "      <td>1.000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td># N's per 100 kbp</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "      <td>0.00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td># mismatches per 100 kbp</td>\n",
       "      <td>44.98</td>\n",
       "      <td>4.82</td>\n",
       "      <td>0.73</td>\n",
       "      <td>0.26</td>\n",
       "      <td>1.03</td>\n",
       "      <td>1.82</td>\n",
       "      <td>1.64</td>\n",
       "      <td>1.64</td>\n",
       "      <td>1.88</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td># indels per 100 kbp</td>\n",
       "      <td>661.17</td>\n",
       "      <td>147.00</td>\n",
       "      <td>27.72</td>\n",
       "      <td>10.04</td>\n",
       "      <td>0.33</td>\n",
       "      <td>0.35</td>\n",
       "      <td>0.22</td>\n",
       "      <td>0.35</td>\n",
       "      <td>0.31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>Largest alignment</td>\n",
       "      <td>149598</td>\n",
       "      <td>517261</td>\n",
       "      <td>3025639</td>\n",
       "      <td>3023270</td>\n",
       "      <td>221546</td>\n",
       "      <td>236202</td>\n",
       "      <td>236202</td>\n",
       "      <td>236202</td>\n",
       "      <td>236106</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>Total aligned length</td>\n",
       "      <td>3539867</td>\n",
       "      <td>4598808</td>\n",
       "      <td>4641139</td>\n",
       "      <td>4646042</td>\n",
       "      <td>4554465</td>\n",
       "      <td>4567861</td>\n",
       "      <td>4568479</td>\n",
       "      <td>4568802</td>\n",
       "      <td>4569910</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>NA50</td>\n",
       "      <td>47768</td>\n",
       "      <td>243589</td>\n",
       "      <td>3025639</td>\n",
       "      <td>3023270</td>\n",
       "      <td>129054</td>\n",
       "      <td>152878</td>\n",
       "      <td>152878</td>\n",
       "      <td>152878</td>\n",
       "      <td>152878</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>NGA50</td>\n",
       "      <td>39743</td>\n",
       "      <td>243589</td>\n",
       "      <td>3025639</td>\n",
       "      <td>3023270</td>\n",
       "      <td>129054</td>\n",
       "      <td>133254</td>\n",
       "      <td>133254</td>\n",
       "      <td>152878</td>\n",
       "      <td>133254</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>NA75</td>\n",
       "      <td>28161</td>\n",
       "      <td>174377</td>\n",
       "      <td>939045</td>\n",
       "      <td>931200</td>\n",
       "      <td>60768</td>\n",
       "      <td>95400</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "      <td>95400</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>NGA75</td>\n",
       "      <td>8918</td>\n",
       "      <td>174377</td>\n",
       "      <td>939045</td>\n",
       "      <td>931200</td>\n",
       "      <td>59669</td>\n",
       "      <td>88325</td>\n",
       "      <td>99738</td>\n",
       "      <td>99738</td>\n",
       "      <td>88325</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>LA50</td>\n",
       "      <td>26</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>14</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>LGA50</td>\n",
       "      <td>38</td>\n",
       "      <td>6</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>14</td>\n",
       "      <td>13</td>\n",
       "      <td>13</td>\n",
       "      <td>12</td>\n",
       "      <td>13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>LA75</td>\n",
       "      <td>48</td>\n",
       "      <td>11</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>26</td>\n",
       "      <td>22</td>\n",
       "      <td>22</td>\n",
       "      <td>22</td>\n",
       "      <td>22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>LGA75</td>\n",
       "      <td>93</td>\n",
       "      <td>11</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>27</td>\n",
       "      <td>23</td>\n",
       "      <td>22</td>\n",
       "      <td>22</td>\n",
       "      <td>23</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                       Assembly pacbio10.contigs pacbio20.contigs  \\\n",
       "0           # contigs (>= 0 bp)               94               22   \n",
       "1        # contigs (>= 1000 bp)               94               22   \n",
       "2        # contigs (>= 5000 bp)               92               22   \n",
       "3       # contigs (>= 10000 bp)               89               21   \n",
       "4       # contigs (>= 25000 bp)               55               20   \n",
       "5       # contigs (>= 50000 bp)               24               18   \n",
       "6        Total length (>= 0 bp)          3540004          4598820   \n",
       "7     Total length (>= 1000 bp)          3540004          4598820   \n",
       "8     Total length (>= 5000 bp)          3530802          4598820   \n",
       "9    Total length (>= 10000 bp)          3506582          4591727   \n",
       "10   Total length (>= 25000 bp)          2917321          4575443   \n",
       "11   Total length (>= 50000 bp)          1757051          4506249   \n",
       "12                    # contigs               94               22   \n",
       "13               Largest contig           176275           751732   \n",
       "14                 Total length          3540004          4598820   \n",
       "15             Reference length          4639675          4639675   \n",
       "16                       GC (%)            50.40            50.76   \n",
       "17             Reference GC (%)            50.79            50.79   \n",
       "18                          N50            49862           273171   \n",
       "19                         NG50            41894           273171   \n",
       "20                          N75            30852           199323   \n",
       "21                         NG75            10787           199323   \n",
       "22                          L50               25                5   \n",
       "23                         LG50               37                5   \n",
       "24                          L75               46               10   \n",
       "25                         LG75               87               10   \n",
       "26              # misassemblies               10                8   \n",
       "27       # misassembled contigs                6                3   \n",
       "28  Misassembled contigs length           357608          1189535   \n",
       "29        # local misassemblies                1                3   \n",
       "30     # scaffold gap ext. mis.                0                0   \n",
       "31     # scaffold gap loc. mis.                0                0   \n",
       "32     # unaligned mis. contigs                0                0   \n",
       "33          # unaligned contigs       0 + 0 part       0 + 0 part   \n",
       "34             Unaligned length                0                0   \n",
       "35          Genome fraction (%)           76.336           98.850   \n",
       "36            Duplication ratio            1.000            1.003   \n",
       "37            # N's per 100 kbp             0.00             0.00   \n",
       "38     # mismatches per 100 kbp            44.98             4.82   \n",
       "39         # indels per 100 kbp           661.17           147.00   \n",
       "40            Largest alignment           149598           517261   \n",
       "41         Total aligned length          3539867          4598808   \n",
       "42                         NA50            47768           243589   \n",
       "43                        NGA50            39743           243589   \n",
       "44                         NA75            28161           174377   \n",
       "45                        NGA75             8918           174377   \n",
       "46                         LA50               26                6   \n",
       "47                        LGA50               38                6   \n",
       "48                         LA75               48               11   \n",
       "49                        LGA75               93               11   \n",
       "\n",
       "   pacbio40.contigs pacbio80.contigs illumina_contigs  \\\n",
       "0                 1                1              167   \n",
       "1                 1                1               87   \n",
       "2                 1                1               62   \n",
       "3                 1                1               57   \n",
       "4                 1                1               47   \n",
       "5                 1                1               31   \n",
       "6           4641141          4649321          4567161   \n",
       "7           4641141          4649321          4548539   \n",
       "8           4641141          4649321          4493976   \n",
       "9           4641141          4649321          4458325   \n",
       "10          4641141          4649321          4312386   \n",
       "11          4641141          4649321          3762852   \n",
       "12                1                1               97   \n",
       "13          4641141          4649321           221601   \n",
       "14          4641141          4649321          4555330   \n",
       "15          4639675          4639675          4639675   \n",
       "16            50.78            50.80            50.74   \n",
       "17            50.79            50.79            50.79   \n",
       "18          4641141          4649321           129054   \n",
       "19          4641141          4649321           129054   \n",
       "20          4641141          4649321            60768   \n",
       "21          4641141          4649321            59669   \n",
       "22                1                1               14   \n",
       "23                1                1               14   \n",
       "24                1                1               26   \n",
       "25                1                1               27   \n",
       "26                8                8                0   \n",
       "27                1                1                0   \n",
       "28          4641141          4649321                0   \n",
       "29                2                2                4   \n",
       "30                0                0                0   \n",
       "31                0                0                0   \n",
       "32                0                0                0   \n",
       "33       0 + 0 part       0 + 0 part       1 + 0 part   \n",
       "34                0                0              542   \n",
       "35           99.995           99.998           98.142   \n",
       "36            1.000            1.002            1.000   \n",
       "37             0.00             0.00             0.00   \n",
       "38             0.73             0.26             1.03   \n",
       "39            27.72            10.04             0.33   \n",
       "40          3025639          3023270           221546   \n",
       "41          4641139          4646042          4554465   \n",
       "42          3025639          3023270           129054   \n",
       "43          3025639          3023270           129054   \n",
       "44           939045           931200            60768   \n",
       "45           939045           931200            59669   \n",
       "46                1                1               14   \n",
       "47                1                1               14   \n",
       "48                2                2               26   \n",
       "49                2                2               27   \n",
       "\n",
       "   illumina_pacbio10_contigs illumina_pacbio20_contigs  \\\n",
       "0                        145                       140   \n",
       "1                         63                        62   \n",
       "2                         46                        47   \n",
       "3                         45                        46   \n",
       "4                         39                        39   \n",
       "5                         29                        30   \n",
       "6                    4580922                   4581204   \n",
       "7                    4564350                   4566832   \n",
       "8                    4526103                   4538061   \n",
       "9                    4518046                   4529247   \n",
       "10                   4439862                   4434562   \n",
       "11                   4111348                   4140604   \n",
       "12                        70                        66   \n",
       "13                    349819                    349819   \n",
       "14                   4568726                   4569348   \n",
       "15                   4639675                   4639675   \n",
       "16                     50.76                     50.76   \n",
       "17                     50.79                     50.79   \n",
       "18                    154542                    154542   \n",
       "19                    154542                    152878   \n",
       "20                     99738                     99738   \n",
       "21                     95450                     99738   \n",
       "22                        11                        11   \n",
       "23                        11                        12   \n",
       "24                        20                        21   \n",
       "25                        21                        21   \n",
       "26                         3                         1   \n",
       "27                         3                         1   \n",
       "28                    808786                    349819   \n",
       "29                         4                         4   \n",
       "30                         0                         0   \n",
       "31                         0                         0   \n",
       "32                         0                         0   \n",
       "33                1 + 0 part                1 + 0 part   \n",
       "34                       542                       542   \n",
       "35                    98.439                    98.457   \n",
       "36                     1.000                     1.000   \n",
       "37                      0.00                      0.00   \n",
       "38                      1.82                      1.64   \n",
       "39                      0.35                      0.22   \n",
       "40                    236202                    236202   \n",
       "41                   4567861                   4568479   \n",
       "42                    152878                    152878   \n",
       "43                    133254                    133254   \n",
       "44                     95400                     99738   \n",
       "45                     88325                     99738   \n",
       "46                        12                        12   \n",
       "47                        13                        13   \n",
       "48                        22                        22   \n",
       "49                        23                        22   \n",
       "\n",
       "   illumina_pacbio40_contigs illumina_pacbio80_contigs  \n",
       "0                        135                       136  \n",
       "1                         59                        60  \n",
       "2                         44                        44  \n",
       "3                         44                        44  \n",
       "4                         38                        37  \n",
       "5                         30                        29  \n",
       "6                    4581146                   4582009  \n",
       "7                    4567604                   4568712  \n",
       "8                    4538834                   4537248  \n",
       "9                    4538834                   4537248  \n",
       "10                   4460648                   4442027  \n",
       "11                   4182994                   4168651  \n",
       "12                        63                        64  \n",
       "13                    349819                    349819  \n",
       "14                   4570120                   4571228  \n",
       "15                   4639675                   4639675  \n",
       "16                     50.76                     50.76  \n",
       "17                     50.79                     50.79  \n",
       "18                    154542                    154542  \n",
       "19                    152878                    154542  \n",
       "20                     99738                     99738  \n",
       "21                     99738                     99738  \n",
       "22                        11                        11  \n",
       "23                        12                        11  \n",
       "24                        21                        20  \n",
       "25                        21                        20  \n",
       "26                         1                         3  \n",
       "27                         1                         3  \n",
       "28                    349819                    855583  \n",
       "29                         5                         6  \n",
       "30                         0                         0  \n",
       "31                         0                         0  \n",
       "32                         0                         0  \n",
       "33                1 + 0 part                1 + 0 part  \n",
       "34                       542                       542  \n",
       "35                    98.476                    98.499  \n",
       "36                     1.000                     1.000  \n",
       "37                      0.00                      0.00  \n",
       "38                      1.64                      1.88  \n",
       "39                      0.35                      0.31  \n",
       "40                    236202                    236106  \n",
       "41                   4568802                   4569910  \n",
       "42                    152878                    152878  \n",
       "43                    152878                    133254  \n",
       "44                     99738                     95400  \n",
       "45                     99738                     88325  \n",
       "46                        12                        12  \n",
       "47                        12                        13  \n",
       "48                        22                        22  \n",
       "49                        22                        23  "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "quast_data = pd.read_csv('quast_result/report.tsv', sep='\\t')\n",
    "quast_data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "1) **# contigs:** лучшее - pacbio40, pacbio80, худшие значения - pacbio10, illumina <br>\n",
    "2) **Largest contig:** лучшее - pacbio40, pacbio80, худшие значения - pacbio10, illumina <br>\n",
    "3) **Total length:** лучшее - pacbio40, pacbio80, но остальные значения, кроме pacbio10, также хорошие <br>\n",
    "4) **N50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "5) **NG50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "6) **N75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "7) **NG75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "8) **L50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "9) **LG50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "10) **L75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "11) **LG75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10, неплохое значение по сравнению с другими показывает pacbio20 <br>\n",
    "12) **# misassemblies:** здесь лучшие значения показывают illumina, illumina+pacbio20, illumina+pacbio40, худшие - все pacbio <br>\n",
    "13) **# misassembled contigs:** лучшее - pacbio40, pacbio80, illumina, illumina+pacbio20, illumina+pacbio40, остальные значения приемлемы <br>\n",
    "14) **# local misassemblies:** лучшее - pacbio10, pacbio40, pacbio80, остальные значения приемлемы <br>\n",
    "15) **# unaligned contigs & unaligned length:** лучшее - все pacbio, остальные значения также хорошие <br>\n",
    "16) **Genome fraction:** лучшее - pacbio40, pacbio80, остальные значения, кроме pacbio10, также очень хорошие <br>\n",
    "17) **Duplication ratio:** лучшие значения показали все, кроме pacbio20 и pacbio80 <br>\n",
    "18) **# mismatches per 100 kbp:** лучшее - pacbio40, pacbio80, приемлемое значение показывает illumina, худшее значение - pacbio10 <br>\n",
    "19) **# indels per 100 kbp:** лучшее - illumina и гибридные сборки, худшее значение - pacbio10 <br>\n",
    "20) **Largest alignment:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "21) **Total aligned length:** лучшее - pacbio40, pacbio80, но остальные значения, кроме pacbio10, также хорошие <br>\n",
    "22) **NA50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "23) **NGA50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "24) **NA75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "25) **NGA75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "26) **LA50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "27) **LGA50:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "28) **LA75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>\n",
    "29) **LGA75:** лучшее - pacbio40, pacbio80, худшее значение - pacbio10 <br>"
   ]
  },
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   "source": [
    "Таким образом, лучшие сборки по метрикам - pacbio40, pacbio80, худшая - pacbio10 (видимо, из-за низкого покрытия)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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