Htstream
Introduction
Htstream
is a quality control and processing pipeline for High Throughput Sequencing data.
For more information, please check its website: https://biocontainers.pro/tools/htstream and its home page on Github.
Versions
1.3.3
Commands
hts_AdapterTrimmer
hts_CutTrim
hts_LengthFilter
hts_NTrimmer
hts_Overlapper
hts_PolyATTrim
hts_Primers
hts_QWindowTrim
hts_SeqScreener
hts_Stats
hts_SuperDeduper
Module
You can load the modules by:
module load biocontainers
module load htstream
Example job
Warning
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 Htstream on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=htstream
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers htstream