bbmap
BBTools genomic aligner and other tools for short sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
bbduk.shbbmap.shbbnorm.shbloomfilter.shdedupe.shreformat.sh
About bbmap
From Debian's package description
The BBTools are a collection of small programs to solve recurrent tasks for the creative handling of short biological RNA/DNA sequences. This suite may be best known for its mapper, which is also the name of the project on sourceforge, but several tools have been added over time. All tools are multi-threaded, implemented platform-independently in Java:
BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels.
BBNorm: Kmer-based error-correction and normalization tool.
Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity.
Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s.
BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file.
From Debian's description of the bbmap package, under that package's license.
Dependencies
Depends on
libmpj-javadefault-jre-headlessorjava-runtime-headless
Recommends
Related apps
- samtoolsprocessing sequence alignments in SAM, BAM and CRAM formatsCommand line
- FastQC quality controlquality control for high throughput sequence data
- bowtie2ultrafast memory-efficient short read alignerCommand line
- bowtieUltrafast memory-efficient short read alignerCommand line
SeaViewEdits multiple sequence alignments and prints them in PostScript format.- minimap2versatile pairwise aligner for genomic and spliced nucleotide sequencesCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the bbmap package, under that package's license.
- Description: Debian's description of the bbmap 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.