hisat2

name	hisat2
description	Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.
disable-model-invocation	true
user-invocable	true

hisat2

Quick Start

• Command: hisat2 [options]* -x <ht2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2
• Version: 2.2.2
• Full reference: See references/help.md for complete options and usage details

When To Use This Tool

• Splice-aware RNA-seq alignment against a HISAT2 index.
• Graph-aware alignment when splice sites, SNPs, or haplotypes are built into the index.
• A common choice for transcript assembly-oriented RNA workflows.
• Pair with hisat2-build when you need to create or rebuild the index.

Common Patterns

# 1) Standard paired-end RNA-seq alignment
hisat2 \
  -x ref_index \
  -1 sample_R1.fastq.gz \
  -2 sample_R2.fastq.gz \
  -p 16 \
  -S sample.sam

# 2) Transcript-assembly friendly output
hisat2 \
  -x ref_index \
  -1 sample_R1.fastq.gz \
  -2 sample_R2.fastq.gz \
  --dta \
  --summary-file sample.hisat2.summary.txt \
  -S sample.sam

# 3) Supply known splice sites
hisat2 \
  -x ref_index \
  --known-splicesite-infile splicesites.txt \
  -U sample.fastq.gz \
  -S sample.sam

Recommended Workflow

1. Build the index first, optionally including splice and exon annotation.
2. Align reads with explicit thread count and summary capture.
3. Use --dta when the output is headed into transcript assembly workflows.
4. Review summary statistics and splice-aware behavior before counting or assembly.

Guardrails

• The -x value is the index basename, not a literal .ht2 filename.
• --no-spliced-alignment is for DNA-like use cases, not ordinary RNA-seq.
• Large -k or --max-seeds values can slow alignment dramatically on repetitive genomes.
• Set --rna-strandness deliberately when the library is stranded; do not guess after the fact.