recipe bbmap

BBMap is a short read aligner, as well as various other bioinformatic tools.

Homepage:

https://sourceforge.net/projects/bbmap

Documentation:

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/

License:

UC-LBL license (see package)

Recipe:

/bbmap/meta.yaml

Links:

biotools: bbmap, doi: 10.1371/journal.pone.0185056

package bbmap

Versions:

39.01-1,  39.01-0,  39.00-0,  38.99-0,  38.98-1,  38.98-0,  38.97-1,  38.97-0,  38.96-1, 

39.01-1,  39.01-0,  39.00-0,  38.99-0,  38.98-1,  38.98-0,  38.97-1,  38.97-0,  38.96-1,  38.96-0,  38.95-1,  38.95-0,  38.93-0,  38.92-0,  38.91-1,  38.91-0,  38.90-3,  38.90-2,  38.90-1,  38.90-0,  38.89-0,  38.88-0,  38.87-0,  38.86-0,  38.84-1,  38.84-0,  38.79-0,  38.76-0,  38.75-0,  38.73-0,  38.72-0,  38.71-0,  38.70-0,  38.69-0,  38.68-0,  38.67-0,  38.65-0,  38.63-0,  38.62-0,  38.61b-0,  38.58-0,  38.57-0,  38.56-0,  38.51-0,  38.49-0,  38.46-0,  38.45-0,  38.44-0,  38.22-1,  38.22-0,  38.20-0,  38.19-0,  38.18-0,  38.16-0,  38.06-2,  38.06-0,  37.99-1,  37.99-0,  37.96-0,  37.95-0,  37.90-0,  37.78-0,  37.77-0,  37.75-0,  37.66-0,  37.62-2,  37.62-1,  37.62-0,  37.52-1,  37.52-0,  37.17-1,  37.17-0,  37.10-1,  37.10-0,  37.02-0,  36.84-0,  36.32-0,  35.85-2,  35.85-1

Depends:

• bzip2 >=1.0.8,<2.0a0

• libgcc-ng >=12

• openjdk >=7.0

• pbzip2

• samtools

Required By:

• phyloflash

• mintie

• bactopia-gather

• busco

• captus

• phame

• aviary

• star-fusion

• xyalign

• metagenome-atlas

• metacerberus

• disco

• wgfast

• hocort

• beav

• itsxpress

• bactopia-qc

• hybpiper

• drax

• zga

• hafez

• metawatt

• jaffa

• etoki

• illumina-cleanup

• confindr

• fusioncatcher

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bbmap

and update with:

conda update bbmap

or use the docker container:

docker pull quay.io/biocontainers/bbmap:<tag>

(see bbmap/tags for valid values for <tag>)

Notes

BBMap is a series of Java programs, but they come with a number of custom wrapper shell scripts. Each of these is symlinked to the conda bin directory during install.

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