HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts. HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover the whole genome (each index represents a genomic region of 64,000 bp and 48,000 indexes are needed to cover the human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively low ( 4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the operations on the FM index.
Keywords for this software
References in zbMATH (referenced in 5 articles )
Showing results 1 to 5 of 5.
- Akalin, Altuna: Computational genomics with R. With the assistance of Verdan Franke, Bora Uyar and Jonathan Ronen (2021)
- Kuan-Hao Chao, Yi-Wen Hsiao, Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow (2019) arXiv
- Wolff, Alexander: Analysis of expression profile and gene variation via development of methods for next generation sequencing data (2018)
- Sirén, Jouni: Indexing variation graphs (2017)
- Matthew J. Wakefield: Xenomapper: Mapping reads in a mixed species context (2016) not zbMATH