GATB-Minia-Pipeline

GATB-Minia-Pipeline is a de novo multi-k assembly pipeline for Illumina data. It can assemble genomes and metagenomes. The pipeline consists of:

• Bloocoo (error correction)
• Minia 3 (contigs assembly) based on the BCALM2 (unitigs assembly) tool
• BESST (scaffolding)

Prerequisites

• Linux 64 bits (for Minia binary)

• bwa (for BESST)

• Python >= 2.7 and < 3 with the following modules (for BESST). See next section for a quick way to install them.

  • mathstats
  • scipy
  • networkx
  • pysam

Installation

pip install --user mathstats networkx scipy pyfasta pysam==0.8.3

git clone --recursive https://github.com/GATB/gatb-minia-pipeline

cd gatb-minia-pipeline ; make test

Usage

Command line arguments are similar to SPAdes.

Paired reads assembly:

./gatb -1 read_1.fastq -2 read_2.fastq

paired-end reads given in a single file:

./gatb --12 interleaved_reads.fastq

Unpaired reads:

./gatb -s single_reads.fastq

The final assembly is in:

assembly.fasta

All other files are intermediary.

More input options are available. Type ./gatb for extended usage.

Since the pipeline is multi-k, it is unnecessary to specify a kmer size.

Install FAQ

Don't copy the ./gatb script to a bin folder it is meant to stay in that directory.

If you have trouble compiling, just give up and ignore the scaffolding (BESST) step. Did you consider that getting contigs instead of scaffolds may be good enough?

If you want to persist compiling, read on.

Can't install scipy? (because e.g. cannot sudo) A solution is to install a python distribution that doesn't require root (it's not that hard).

Conda:

wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
sh Miniconda-latest-Linux-x86_64.sh
. ~/.bashrc
conda install scipy pysam networkx
pip install mathstats

Read more on conda : http://lh3.github.io/2015/12/07/bioconda-the-best-package-manager-so-far/

http://conda.pydata.org/miniconda.html

Alternative: activestate python (http://www.activestate.com/activepython/downloads then type pypm install scipy)

Support

To contact an author directly: [email protected] Community support: https://www.biostars.org/t/GATB/