gmap
spliced and SNP-tolerant alignment for mRNA and short reads
Command lineScience
Not tested on a device yet. What that means
Commands in the package
gmapgmap.nosimdgmap_buildgmaplgmapl.nosimdgsnapgsnap.nosimdgsnaplgsnapl.nosimd
About gmap
From Debian's package description
This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of
- known splice sites and identify novel splice sites.
- known single-nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.
From Debian's description of the gmap package, under that package's license.
Dependencies
Depends on
perllibbz2-1.0libc6zlib1g
Related apps
- bowtie2ultrafast memory-efficient short read alignerCommand line
- bioperlPerl tools for computational molecular biologyCommand line
- bowtieUltrafast memory-efficient short read alignerCommand line
- hisat2graph-based alignment of short nucleotide reads to many genomesCommand line
- minimap2versatile pairwise aligner for genomic and spliced nucleotide sequencesCommand line
- hhsuitesensitive protein sequence searching based on HMM-HMM alignmentCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the gmap package, under that package's license.
- Description: Debian's description of the gmap 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.