hisat2-align-l

name	hisat2-align-l
description	Use when aligning RNA-seq reads to a reference genome using a HISAT2 index, particularly for splice-aware alignment of transcriptomic data.
disable-model-invocation	true
user-invocable	true

hisat2-align-l

Quick Start

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

When To Use This Tool

• Use hisat2-align-l when aligning reads against a HISAT2 large index (.ht2l), typically for very large references or graph-aware indexes.
• It is especially appropriate for splice-aware RNA-seq alignment, including workflows that use known splice sites or downstream transcript assembly.
• Use it when you intentionally need the large-index binary rather than the generic hisat2 wrapper.
• For DNA-style alignment, pair this with --no-spliced-alignment; otherwise spliced alignment behavior remains active by default.

Common Patterns

# Splice-aware single-end alignment against a large index
hisat2-align-l -x genome_large -U reads.fq -S aln.sam

# Paired-end RNA-seq alignment with transcript-assembler friendly output
hisat2-align-l -x genome_large -1 reads_R1.fq -2 reads_R2.fq --dta -p 8 -S aln.sam

# Provide known splice sites to guide alignment
hisat2-align-l -x genome_large -U reads.fq --known-splicesite-infile splicesites.txt -S aln.sam

# DNA-style alignment with spliced alignment disabled
hisat2-align-l -x genome_large -U reads.fq --no-spliced-alignment -S aln.sam

Recommended Workflow

1. Prepare a HISAT2 index using hisat2-build (produces .ht2l files referenced via prefix with -x)
2. Choose appropriate preset (--fast, --sensitive, or --very-sensitive) based on speed vs. sensitivity tradeoff
3. Run alignment specifying index prefix, input reads, and output SAM file: hisat2-align-l -x genome -1 reads_1.fq -2 reads_2.fq -S output.sam
4. Review alignment summary (printed to stderr or via --summary-file) for mapping statistics

Guardrails

• Running hisat2-align-l directly is not recommended; prefer the hisat2 wrapper script for typical use cases
• Large values for -k (max alignments per read) or --max-seeds can significantly slow alignment on repetitive genomes
• Thread count (-p/--threads) defaults to 1; increase for multi-core systems but match available resources
• Paired-end fragment bounds -I/-X are only valid with --no-spliced-alignment