Stacks-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.48, 2.0

Author / Distributor

Stacks

Description

"Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography." More details are at Stacks

Running Program

The last version of this application is at /usr/local/apps/eb/Stacks/2.0-foss-2016b

To use this version, please load the module with

ml Stacks/2.0-foss-2016b 

To use the older version, namely v. 1.48, please first load the module with

ml Stacks/1.48-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_Stacks
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=Stacks.%j.out
#SBATCH --error=Stacks.%j.err

cd $SLURM_SUBMIT_DIR
ml Stacks/2.0-foss-2016b
sstacks [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml Stacks/2.0-foss-2016b 
sstacks -h
sstacks 2.0
sstacks -P dir -M popmap [-p n_threads]
sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads]
  -P,--in_path: path to the directory containing Stacks files.
  -M,--popmap: path to a population map file from which to take sample names.
  -s,--sample: filename prefix from which to load sample loci.
  -c,--catalog: path to the catalog.
  -p,--threads: enable parallel execution with num_threads threads.
  -o,--out_path: output path to write results.
  -x: don't verify haplotype of matching locus.

Gapped assembly options:
  --disable_gapped: disable gapped alignments between stacks (default: enable gapped alignments).

ml Stacks/1.48-foss-2016b 
sstacks -h
sstacks 1.48
sstacks [--aligned] -P dir [-b batch_id] -M popmap [-p n_threads]
sstacks [--aligned] -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads]
  b: database/batch ID of the catalog to consider (default: guess).
  P: path to the directory containing Stacks files.
  M: path to a population map file from which to take sample names.
  s: filename prefix from which to load sample loci.
  c: path to the catalog.
  g,--aligned: base matching on alignment position, not sequence identity.
  p: enable parallel execution with num_threads threads.
  o: output path to write results.
  x: don't verify haplotype of matching locus.

Gapped assembly options:
  --gapped: preform gapped alignments between stacks.

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Installation

Source code is obtained from Stacks

System

64-bit Linux