hisat2
graph-based alignment of short nucleotide reads to many genomes
Command lineScience
Not tested on a device yet. What that means
Commands in the package
hisat2hisat2-align-lhisat2-align-shisat2-buildhisat2-build-lhisat2-build-shisat2-inspecthisat2-inspect-lhisat2-inspect-s
About hisat2
From Debian's package description
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 against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. 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).
From Debian's description of the hisat2 package, under that package's license.
Dependencies
Depends on
Recommends
Related apps
- mummerEfficient sequence alignment of full genomesCommand line
- gbrowseGMOD Generic Genome BrowserCommand line
- samtoolsprocessing sequence alignments in SAM, BAM and CRAM formatsCommand line
- bowtie2ultrafast memory-efficient short read alignerCommand line
- sra-toolkitutilities for the NCBI Sequence Read ArchiveCommand line
- mafftMultiple alignment program for amino acid or nucleotide sequencesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the hisat2 package, under that package's license.
- Description: Debian's description of the hisat2 package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.