hisat2-align-s

name	hisat2-align-s
description	Use when aligning RNA-seq reads to a HISAT2 index using the alignment binary directly. Supports spliced alignment with optional splice site annotation.
disable-model-invocation	true
user-invocable	true

hisat2-align-s

Quick Start

• Command: hisat2-align-s -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2-align-s
• Full options: see references/help.md

When To Use This Tool

• Use hisat2-align-s when aligning reads against a standard HISAT2 small index (.ht2).
• It is a good fit for splice-aware RNA-seq alignment, especially when you want to inject known splice sites or produce --dta output for transcript assemblers.
• Use it when you explicitly want the small-index binary rather than the generic hisat2 wrapper.
• For non-RNA or strictly contiguous alignments, disable splice handling with --no-spliced-alignment.

Common Patterns

# 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

Recommended Workflow

1. Build or obtain a HISAT2 index (.ht2 files) for your reference genome
2. Prepare input reads as FASTQ/FASTA; specify paired mates with -1 and -2, or unpaired with -U
3. Run alignment with appropriate options (e.g., --dta for transcript assemblers, -p for threads, --known-splicesite-infile if available)
4. Redirect or specify SAM output with -S; process downstream with samtools or transcript assemblers

Guardrails

• The tool warns that running hisat2-align directly is not recommended; prefer the hisat2 wrapper script for typical use
• Large values for -k or --max-seeds can significantly slow alignment on repetitive genomes
• Spliced alignment is enabled by default; use --no-spliced-alignment only for DNA-read alignment scenarios
• -I/-X fragment-length options only apply when spliced alignment is disabled