ngmlr
CoNvex Gap-cost alignMents for Long Reads
Command lineScience
Not tested on a device yet. What that means
Commands in the package
ngmlr
About ngmlr
From Debian's package description
Ngmlr is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith- Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments.
From Debian's description of the ngmlr package, under that package's license.
Dependencies
Depends on
libc6libgcc-s1libssw0libstdc++6zlib1g
Related apps
- qhull-bincalculate convex hulls and related structures (utilities)Command line
- gap-coreGAP computer algebra system, core componentsCommand line
- lrslibpackage to enumerate vertices and extreme rays of a convex polyhedronCommand line
- dascrubberalignment-based scrubbing pipeline for DNA sequencing readsCommand line
- gmapspliced and SNP-tolerant alignment for mRNA and short readsCommand line
- raconconsensus module for raw de novo DNA assembly of long uncorrected readsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the ngmlr package, under that package's license.
- Description: Debian's description of the ngmlr 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.