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 and its home page on Github.
Versions¶
2.2.1
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
Module¶
You can load the modules by:
module load biocontainers
module load hisat2
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 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