Use when aligning RNA-seq reads to a HISAT2 index using the alignment binary directly. Supports spliced alignment with optional splice site annotation.
hisat2-align-s -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]/home/vimalinx/miniforge3/envs/bio/bin/hisat2-align-shisat2-align-s when aligning reads against a standard HISAT2 small index (.ht2).--dta output for transcript assemblers.hisat2 wrapper.--no-spliced-alignment.# Single-end splice-aware alignment
hisat2-align-s -x genome -U reads.fq -S aln.sam
# Paired-end RNA-seq alignment with 8 threads
hisat2-align-s -x genome -1 reads_R1.fq -2 reads_R2.fq -p 8 -S aln.sam
# Guide alignment with known splice sites and transcript-assembler output
hisat2-align-s -x genome -U reads.fq --known-splicesite-infile splicesites.txt --dta -S aln.sam
# DNA-style alignment without spliced alignment
hisat2-align-s -x genome -U reads.fq --no-spliced-alignment -S aln.sam
.ht2 files) for your reference genome-1 and -2, or unpaired with -U--dta for transcript assemblers, -p for threads, --known-splicesite-infile if available)-S; process downstream with samtools or transcript assemblershisat2-align directly is not recommended; prefer the hisat2 wrapper script for typical use-k or --max-seeds can significantly slow alignment on repetitive genomes--no-spliced-alignment only for DNA-read alignment scenarios-I/-X fragment-length options only apply when spliced alignment is disabled