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Repository hisat2
Name: hisat2
Owner: iuc
Synopsis: HISAT2 is a fast and sensitive spliced alignment program.
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 [SirĂ©n 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).
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Contents of this repository

Name Description Version Minimum Galaxy Version
A fast and sensitive alignment program 2.1.0+galaxy3 17.01

Assembly - Tools for working with assemblies