deconseq
Link to section 'Introduction' of '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.
Home page: http://deconseq.sourceforge.net/
Link to section 'Versions' of 'deconseq' Versions
- 0.4.3
Link to section 'Commands' of 'deconseq' Commands
- bwa64
- deconseq.pl
- splitFasta.pl
Link to section 'Module' of 'deconseq' Module
You can load the modules by:
module load biocontainers
module load deconseq
Helper command
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/).
Link to section 'Example job' of 'deconseq' Example job
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