HISAT2¶
Description¶
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). It uses an original approach of a graph FM index (GFM) based on an extension of BWT for graphs [Sirén et al. 2014]. In addition to using one global GFM index that represents the general population, HISAT2 uses a large set of small 56Kbp GFM indexes to cover the whole genome. These local, 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).
Environment Modules¶
Run module spider hisat2 to find out what environment modules are available for this application.
Environment Variables¶
- HPC_HISAT2_DIR - installation directory
- HPC_HISAT2_BIN - executable directory
- HPC_HISAT2_DOC - documentation directory
- HPC_HISAT2_EXE - examples directory
Citation¶
If you publish research that uses hisat2 you have to cite it as follows:
Categories¶
biology, alignment, ngs