htstream
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'htstream' Versions
- 1.3.3
Link to section 'Commands' of 'htstream' Commands
- hts_AdapterTrimmer
- hts_CutTrim
- hts_LengthFilter
- hts_NTrimmer
- hts_Overlapper
- hts_PolyATTrim
- hts_Primers
- hts_QWindowTrim
- hts_SeqScreener
- hts_Stats
- hts_SuperDeduper
Link to section 'Module' of 'htstream' Module
You can load the modules by:
module load biocontainers
module load htstream
Link to section 'Example job' of 'htstream' 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 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