Deconseq

Introduction

DeconSeq: DECONtamination of SEQuence data using a modified version of BWA-SW. The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

For more information, please check:
Home page: http://deconseq.sourceforge.net/

Versions

  • 0.4.3

Commands

  • bwa64

  • deconseq.pl

  • splitFasta.pl

Module

You can load the modules by:

module load biocontainers
module load deconseq

Helper command

Note

Users need to use DeconSeqConfig.pm to specify the database information. Besides, for the current deconseq module in biocontainers, users need to copy the executables to your current directory, including bwa64, deconseq.pl, and splitFasta.pl. This step is only needed to run once.

A helper command copy_DeconSeqConfig is provided to copy the configuration file DeconSeqConfig.pm and executables to your current directory. You just need to run the command copy_DeconSeqConfig and modify DeconSeqConfig.pm as needed:

copy_DeconSeqConfig
nano DeconSeqConfig.pm # modify database information as needed

For detailed information about how to config DeconSeqConfig.pm, please check its online manual (https://sourceforge.net/projects/deconseq/files/).

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run deconseq on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=deconseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers deconseq

bwa64 index -p hg38_db -a bwtsw Homo_sapiens.GRCh38.dna.fa
bwa64 index -p m39_db -a bwtsw GRCm38.p4.genome.fa
deconseq.pl -f input.fastq -dbs hg38_db -dbs_retain m39_db