plasmidseeker
identification of known plasmids from whole-genome sequencing reads
Command lineScience
Not tested on a device yet. What that means
Commands in the package
plasmidseeker
About plasmidseeker
From Debian's package description
PlasmidSeeker is a k-mer based program for the identification of known plasmids from bacterial whole genome sequencing reads.
PlasmidSeeker that enables the detection of plasmids from bacterial WGS data without read assembly. The PlasmidSeeker algorithm is based on k-mers and uses k-mer abundance to distinguish between plasmid and bacterial sequences. The performance of PlasmidSeeker was tested on a set of simulated and real bacterial WGS samples, resulting in 100% sensitivity and 99.98% specificity.
From Debian's description of the plasmidseeker package, under that package's license.
Dependencies
Depends on
Related apps
- plinkwhole-genome association analysis toolsetCommand line
- cutadaptClean biological sequences from high-throughput sequencing readsCommand line
- dascrubberalignment-based scrubbing pipeline for DNA sequencing readsCommand line
- dazzdbmanage nucleotide sequencing read dataCommand line
- flyede novo assembler for single molecule sequencing reads using repeat graphsCommand line
- cnvkitCopy number variant detection from targeted DNA sequencingCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the plasmidseeker package, under that package's license.
- Description: Debian's description of the plasmidseeker 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.