Software: QTL-seq
Description
Bulked segregant analysis, as implemented in QTL-seq (Takagi et al., 2013), is a powerful and efficient method to identify agronomically important loci in crop plants. QTL-seq was adapted from MutMap to identify quantitative trait loci. It utilizes sequences pooled from two segregating progeny populations with extreme opposite traits (e.g. resistant vs susceptible) and a single whole-genome resequencing of either of the parental cultivars.
Available Versions
| Unspecified: | 2.2.3 |
|---|
BioContainers: https://biocontainers.pro/tools/qtlseq
Home page: https://github.com/YuSugihara/QTL-seq#What-is-QTL-seq
Commands
- qtlseq
Module
You can load the modules by:
module load biocontainers
module load qtlseq
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run qtlseq on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=qtlseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers qtlseq