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A strongly opinionated, iterative, guided contig assembly pipeline. Integrates (+error-correction), bwa-mem, bedtools, and samtools. MPI and multiprocessing aware.
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README.md

itero

A pipeline for iterative, guided contig assembly that integrates spades, bwa, and samtools to produce assembled contigs. MPI and multiprocessing aware.

Documentation

Please see itero.readthedocs.io.

Requirements

If installed using conda, all of the itero dependencies should also be installed. These include:

Python

  • 2.7

Python Modules

3rd-party programs

Installation

Easiest using conda and bioconda. See Documentation for details. Short version, install anaconda or miniconda, then:

# setup bioconda
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

# install itero
conda install itero

# check itero
itero check binaries

Alternative Installation

See Documentation for details. Also installs by cloning/downloading this repository and running:

python setup.py install

This command should install itero and its python dependencies, but you are on your own to install the 3rd-party programs that are also needed. The conda installation automates this process.

Configuration

If you install itero without using conda, itero needs to know the paths to the 3rd-party binaries listed above. You can directly specify the paths (or override the defaults), by creating an ~/.itero.conf file with a format identical to:

[executables]
bedtools:$CONDA_PREFIX/bin/bedtools
bwa:$CONDA_PREFIX/bin/bwa
gawk:$CONDA_PREFIX/bin/gawk
samtools:$CONDA_PREFIX/bin/samtools
spades:$CONDA_PREFIX/bin/spades.py

Execution

itero has both a local mode and an MPI mode. The local mode is for execution on a single node, while the MPI mode executes individual locus assemblies in parallel using an MPI-enabled HPC cluster. To run the program, you must first create a configuration file denoting the samples you wish you assemble. That file has the following format:

[reference]
/path/to/the/locus/seeds.fasta

[individuals]
taxon-one:/path/to/fastq/R1/and/R2/files/for/taxon/1/
taxon-two:/path/to/fastq/R1/and/R2/files/for/taxon/2/
taxon-three:/path/to/fastq/R1/and/R2/files/for/taxon/3/

You then run the local version using a command similar to:

itero assemble local --config ndna-test.conf 
	--output local
	--local-cores 16
	--iterations 6

This will run itero on a single node and will first use 16 cores to perform bwa alignments. The code will then distribute locus-specific assemblies across all cores on the node (1 assembly per core; 16 in parallel).

You run the MPI version using a command similar to:

mpirun -hostfile hostfile -n 96 itero assemble mpi --config ndna-test.conf \
	--output mpi \
	--local-cores 16 \
	--iterations 6

If each of your nodes has 16 cores, this will first use 16 cores for the needed bwa alignments of reads to seeds. The code will then distribute locus-specific assemblies across all 96 cores in your cluster (1 assembly per core; 96 in parallel).

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