Scaffolding pipeline using data from long reads technologies (PacBio, ONT) to scaffold an initial draft assembly. The long reads are shred in smaller segments (f.i. 1000 bp) to create fake mate-pairs. The fake mates are then aligned against the draft assembly and the spinner scaffolder looks for links between contigs and creates scaffolds.

Download and Compile:

Requirements for compiling: Cmake > = 2.6.4

$ git clone https://github.com/SangerHpag/smis.git
$ cd smis 
$ ./makeall.sh

(Tested with gcc-4.9.2, bamtools-2.4.0)

External packages

The smis pipeline downloads and installs the bamtools for reading bam files (https://github.com/pezmaster31/bamtools)

Test using E.coli data

$ cd /full/path/to/smis/example
$ ./run_ecoli_test.sh

The script launch smis in the local smis_test folder scaffolding the draft assembly using ONT fastq data in the smis/example/ecoli_data folder. The results will be in smis/example/smis_test/spinner_scaffolds.fasta and can be compared with the in-house generated scaffolds in smis/ecoli_data/spinner_scaffolds.fasta .

With the default parameters (24 threads) the test takes about 4 minutes.

Run

Setup

$MYSMISDIR/setup.sh </full/path/to/destdir> <draft_assembly> <long_reads>

where:
   /full/path/to/destdir: folder where to run the pipeline (Please provide full path)
   draft assembly: fasta file of the assembly to be scaffolded  (Please provide full path)
   long reads: fastq file of long reads for scaffolding (Please provide full path)

Parameters

The pipeline parameters can be modified in the /full/path/to/destdir/mysettings.sh . The default aligner is bwa. Change to smalt by changing the 'aligner' variable in settings.sh

Run:

Requirements for running: samtools, bwa (or smalt) in PATH.

cd /full/path/to/destdir
./mysmissv.sh

(Tested with samtools-1.3.1, bwa-0.7.12, smalt-0.7.4)

Results

Scaffolds will be in /full/path/to/destdir/spinner_scaffolds.fasta