bash wrapper for running GBS/ddRAD pipeline
Download links for the tools:
- bowtie2 : https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1
- Parallel : https://www.gnu.org/software/parallel/
- sabre : https://github.com/najoshi/sabre
- cutadapt : Recommended to install through bioconda (http://cutadapt.readthedocs.io/en/stable/installation.html)
- bcftools : Recommended to install through bioconda (http://www.htslib.org/download/)
- samtools : Recommended to install through bioconda (http://www.htslib.org/download/)
USAGE: runGBS.pl --se/--pe -r <reference.fa> -k <GBS_KeyFile.txt> -i <fastq_dir_path>
Options:
--se|S - Single-end data
--pe|P - Paired-end data
--reference|-r - Reference sequence file. (.fasta or .fa)
--keyfile|-k - Path for Keyfile.
--fastq|-i - Path for fastq directory (fastq files should named as FLOWCELLIF_LANE.fq.gz)
Fastq processing:
--adapter|-a - Adapter sequence to use for cutadapt tool. (default: GAGATCGGAAGAGCGGG)
--minlength|-m - Minimum read length to be considered. (default: 50)
Performance:
--threads|-p - Number of threads/cores to be used for bowtie2/samtools/bcftools (default: 2)
--npcore|-n - Number of threads/cores to be used for parallel (default: 2)
Tools:
--sabre - Paht for sabre executable (default: $PATH/sabre)
--cutadapt - Paht for cutadapt executable (default: $PATH/cutadapt)
--bowtie2 - Paht for bowtie2 executable (default: $PATH/bowtie2)
--samtools - Paht for samtools executable (default: $PATH/samtools)
--bcftools - Paht for bcftools executable (default: $PATH/bcftools)