discosnp
discovering Single Nucleotide Polymorphism from raw set(s) of reads
Command lineScience
Not tested on a device yet. What that means
Commands in the package
create_coverage_h5_filekissnp2kissreads2run_discoSnp++.shrun_discoSnp++_ML.sh
About discosnp
From Debian's package description
Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP:
1) its mean read coverage 2) the (phred) quality of reads generating the polymorphism.
This program is superseded by DiscoSnp++.
From Debian's description of the discosnp package, under that package's license.
Dependencies
Depends on
Related apps
- gbrowseGMOD Generic Genome BrowserCommand line
- bcftoolsgenomic variant calling and manipulation of VCF/BCF filesCommand line
- coqproof assistant for higher-order logic (toplevel and compiler)Command line
- e00comprProgram to read/write Arcinfo compressed E00 filesCommand line
- pari-gp2cPARI/GP GP to C compilerCommand line
- hisat2graph-based alignment of short nucleotide reads to many genomesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the discosnp package, under that package's license.
- Description: Debian's description of the discosnp 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.