stacks
Link to section 'Introduction' of 'stacks' Introduction
Stacks is a software pipeline for building loci from RAD-seq.
For more information, please check its website: https://biocontainers.pro/tools/stacks.
Link to section 'Versions' of 'stacks' Versions
- 2.60
Link to section 'Commands' of 'stacks' Commands
- clone_filter
- count_fixed_catalog_snps.py
- cstacks
- denovo_map.pl
- gstacks
- integrate_alignments.py
- kmer_filter
- phasedstacks
- populations
- process_radtags
- process_shortreads
- ref_map.pl
- sstacks
- stacks-dist-extract
- stacks-gdb
- stacks-integrate-alignments
- tsv2bam
- ustacks
Link to section 'Module' of 'stacks' Module
You can load the modules by:
module load biocontainers
module load stacks
Link to section 'Example job' of 'stacks' 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 Stacks on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=stacks
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers stacks
denovo_map.pl -T 8 -M 4 -o ./stacks/ \
--samples ./samples --popmap ./popmaps/popmap