HybPiper
HybPiper was designed for targeted sequence capture (Hyb-Seq), in which DNA sequences of interest are enriched from genomic libraries. It recovers the target coding sequences (and optionally flanking regions) from high-throughput sequencing reads, for use in phylogenomics.
License
Free to use and open source under GNU GPLv3.
Available
- Roihu: 2.3.4, via the
bio-appsmodule.
Usage
HybPiper is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the HybPiper module:
For a single sample, assemble the target loci from paired-end reads:
hybpiper assemble -t_dna target_file.fasta -r sample_R1.fastq sample_R2.fastq --prefix sample --cpu 8
Example batch script
#!/bin/bash
#SBATCH --job-name=hybpiper
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=4G
module load bio-apps/v202603
module load hybpiper/2.3.4
hybpiper assemble -t_dna target_file.fasta -r sample_R1.fastq sample_R2.fastq \
--prefix sample --cpu $SLURM_CPUS_PER_TASK
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.