| HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents the general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/hisat2
| Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required) |
| Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required) |
| Repository package_hisat_2_0 revision c65f00072e57 owned by iuc |
| Name | Version | Type | |
|---|---|---|---|
| hisat | 2.0 | package | |
| samtools | 1.2 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| A fast and sensitive alignment program | 1.0.1 | any | |