domains / families / science / hisat2-alignment

hisat2-alignment

separate

Aligns RNA-seq reads to a genome with HISAT2, the splice-aware aligner whose hierarchical graph FM-index runs at roughly a quarter of STAR's memory (~7 GB for human), whose SNP/haplotype graph index reduces reference bias in the index itself, and whose MAPQ is GATK-friendly (60 for unique, no 255 problem). Use when RNA alignment must fit a memory-constrained machine, when feeding StringTie/Cufflinks transcript assembly via --dta, or when a SNP-aware graph index is wanted for allele-robust mapping. Feature-rich/high-RAM RNA alignment and fusion detection are star-alignment; DE on known transcripts only should skip alignment for rna-quantification/alignment-free-quant; the QC gate and contig-naming reconciliation are alignment-files; counting is rna-quantification.

When to use

• low-memory RNA splice-aware mapping
• index building (plain / annotation-aware / SNP-graph)
• strandedness configuration
• --dta transcript-assembly mode
• manual two-pass alignment
• allele-robust mapping with SNP-aware graph index

When not to use

• feature-rich/high-RAM RNA alignment
• fusion detection
• native gene counts
• DE on known transcripts only
• QC gate and contig-naming reconciliation
• counting reads over genes
• DNA alignment
• long read alignment

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