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Repository hisat
Name: hisat
Owner: devteam
Synopsis: HISAT is a fast and sensitive spliced alignment program.
As part of HISAT, we have developed a new indexing scheme based on
the Burrows-Wheeler transform (BWT) and the FM index, called
hierarchical indexing, that employs two types of indexes: (1)
one global FM index representing the whole genome, and (2) many
separate local FM indexes for small regions collectively covering
the genome. Our hierarchical index for the human genome (about 3
billion bp) includes ~48,000 local FM indexes, each representing a
genomic region of ~64,000bp. As the basis for non-gapped alignment,
the FM index is extremely fast with a low memory footprint, as
demonstrated by Bowtie. In addition, HISAT provides several alignment
strategies specifically designed for mapping different types of
RNA-seq reads. All these together, HISAT enables extremely fast and
sensitive alignment of reads, in particular those spanning two exons
or more. As a result, HISAT is much faster >50 times than TopHat2
with better alignment quality. Although it uses a large number of
indexes, the memory requirement of HISAT is still modest,
approximately 4.3 GB for human. HISAT uses the Bowtie2
implementation to handle most of the operations on the FM index.
In addition to spliced alignment, HISAT handles reads involving
indels and supports a paired-end alignment mode. Multiple processor
can be used simultaneously to achieve greater alignment speed.
HISAT outputs alignments in SAM format, enabling interoperation
with a large number of other tools (e.g. SAMtools, GATK) that use
SAM. HISAT is distributed under the GPLv3 license, and it runs on
the command line under Linux, Mac OS X and Windows.
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/hisat
Type: unrestricted
Revision: 3:0505bdb7d6b1
This revision can be installed: True
Times cloned / installed: 2219
Dependencies of this repository

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_0_1_6 revision e1f428b67305 owned by iuc

Name Version Type
hisat 0.1.6 package
samtools 1.2 package

Contents of this repository

Name Description Version Minimum Galaxy Version
spliced aligner 1.0.3 any

Categories
Assembly - Tools for working with assemblies