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Pipeline Assemblage Asselidae Pacbio(hifiasm)

Short description

{ARG} --> argument from the config.yaml or the one you give in your comment see run the pipeline section

Dependancies

• conda
• snakemake

Input

Pacbio Long-reads

The reads should be reunited in a folder and have to be gzipped (fastq.gz) like:

    long_reads_folder
    ├── 01022023.fastq.gz
    ├── fastq_runid_ca9af3b5ba9ac03d97b156b20e01b9f569911a7f_44_0.fastq.gz
    └── fastq_runid_gyfgidgfilga9ac03d97b156b20e01b9f569911a7f_12_0.fastq.gz

You need to give the fullpath to "long_reads_folder" like : /beegfs/data/gdebaecker/Proasellus_coiffaiti/pacbio_fastq/

Run the pipeline

exemple

#!/bin/bash
#SBATCH --partition=normal
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --time=168:00:00
#SBATCH --mem=300G
#SBATCH --output=/beegfs/home/gdebaecker/out_error/pipeline_hifiasm.out
#SBATCH --error=/beegfs/home/gdebaecker/out_error/pipeline_hifiasm.e
#SBATCH --job-name=pipeline_hifiasm
#SBATCH --mail-type=ALL
#SBATCH --mail-user='[email protected]'

source /beegfs/data/soft/bioconda/etc/profile.d/conda.sh
cd /beegfs/project/nega/script_pipeline_gautier/pipeline_pacbio_hifiasm/
FASTQ=/beegfs/data/gdebaecker/Proasellus_coiffaiti/pacbio_reads/test_pipeline
OUTDIR=/beegfs/project/nega/assembly/pipeline_hifiasm

snakemake assembly --use-conda -j 16 -C reads_folder=$FASTQ out_dir=$OUTDIR asm_name="test_proasellus_coiffaiti_hifiasm" busco_db="arthropoda_odb10"

OUTPUT

NANOPLOT

{out_dir}/QC/nanoplot/NanoPlot-report.html --> html report from nanoplot with all the QC stats and graph for the reads

{out_dir}/QC/nanoplot/NanoStats.txt --> small txt file with quick reads stats

HIFIASM

{out_dir}/assembly_hifiasm/{asm_name}.bp.p_ctg.fa --> assembly to use for next step analysis

QUAST

{out_dir}/QC/QUAST/DRAFT_ASSEMBLY/report.tsv --> report file from quast with basic assembly stats like size, N50 , nb contigs etc

BUSCO

{out_dir}/QC/BUSCO/{asm_name}_DRAFT/short_summary.specific.{busco_db}.{asm_name} --> report file from busco

Pipeline Diagram