GATB-Minia-Pipeline

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

• Bloocoo (error correction)
• Minia (contigs assembly)
• 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

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

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

FAQ

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/