hisat2
Link to section 'Introduction' of 'hisat2' Introduction
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.
For more information, please check its website: https://biocontainers.pro/tools/hisat2.
Link to section 'Versions' of 'hisat2' Versions
- 2.2.1
Link to section 'Commands' of 'hisat2' Commands
- extract_exons.py
- extract_splice_sites.py
- hisat2
- hisat2-align-l
- hisat2-align-s
- hisat2-build
- hisat2-build-l
- hisat2-build-s
- hisat2-inspect
- hisat2-inspect-l
- hisat2-inspect-s
- hisat2_extract_exons.py
- hisat2_extract_snps_haplotypes_UCSC.py
- hisat2_extract_snps_haplotypes_VCF.py
- hisat2_extract_splice_sites.py
- hisat2_read_statistics.py
- hisat2_simulate_reads.py
Link to section 'Module' of 'hisat2' Module
You can load the modules by:
module load biocontainers
module load hisat2
Link to section 'Example job' of 'hisat2' 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 HISAT2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hisat2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers hisat2
hisat2-build genome.fa genome
# for single-end FASTA reads DNA alignment
hisat2 -f -x genome -U reads.fa -S output.sam --no-spliced-alignment
# for paired-end FASTQ reads alignment
hisat2 -x genome -1 reads_1.fq -2 read2_2.fq -S output.sam