HISAT: a fast spliced aligner with low memory requirements

By Daehwan Kim, Ben Langmead, Steven L. Salzberg. Nature Methods, 2015

20,246 citations recorded by the source corpus.

HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/176490c7bbb20b5a64aca49d9dc3b75bdfd76d67

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Citations in the corpus

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data (2019, methodology): “All sequencing reads were mapped with hisat (14) v.”
Structural variant calling: the long and the short of it (2019, methodology): “Of note, TopHat is out-dated, and its authors recommend to use HISAT2 [92] instead.”
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease (2018, methodology): “, 2014), then aligned to an Ensembl GRCh38 human genome index with HISAT (Kim et al., 2015).”
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis (2019, methodology): “In particular, we have implemented both the classical spliced aligner––HISAT2 (6), as well as the ultra-fast pseudoalignment based method––kallisto (7) to support raw RNAseq mapping for the 17 species.”
The UCSC Genome Browser database: 2021 update (2020, methodology): “edu/goldenPath/hg19/bigZips/analysisSet/) has been added to the bigZips directory, along with indices for BWA (21,22), Bowtie2 (23), and Hisat2 (24).”