HISAT2 is a fast and sensitive alignment program for mapping
next-generation sequencing reads (both DNA and RNA) to a population
of human genomes (as well as to a single reference genome).
Based on an extension of BWT for graphs, in this module, a graph FM
index (GFM), an original approach and its first implementation to
the best of our knowledge is implemented.
In addition to using one global GFM index that represents a
population of human genomes, 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).
This is the mulithreaded version.
Home : https://ccb.jhu.edu/software/hisat2
Manual/web : https://ccb.jhu.edu/software/hisat2/manual.shtml
Manual/local : /opt/bwhpc/common/bio/hisat2/2.0.4/MANUAL
FAQ : https://ccb.jhu.edu/software/hisat2/faq.shtml
Examples : /opt/bwhpc/common/bio/hisat2/2.0.4/example
The command line executable 'hisat2' of this module can be found in the folder:
The PATH is set to this folder, too.
Type 'hisat2' without any options to see the command-line parameters.
Examples for the usage on bwHPC clusters can be found in:
READ THE FILE
FOR SOME INFOS ABOUT THE EXAMPLES.
In case of problems, please contact 'email@example.com'.