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