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bbmap-software

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BBMap

BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is part of the BBTools project and includes other tools like BBDuk.

Information

Usage

See versions of bbmap which are available:

$ module avail bbmap

Load one version into your environment and run it:

$ module load bbmap/38.67
$ bbmap.sh

Note: BBMap is multithreaded for both indexing and mapping. It will use all available threads on the host unless capped with the t= flag. Please set this to a number that matches the number of CPUs you requested in your SLURM allocation. See the documentation for more information.

Installation

Notes from the sysadmin during installation:

$ cd /tmp/
$ wget 'https://downloads.sourceforge.net/project/bbmap/BBMap_38.67.tar.gz?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbbmap%2Ffiles%2Flatest%2Fdownload&ts=1568205639' -O BBMap_38.67.tar.gz
$ tar xf BBMap_38.67.tar.gz
$ sudo mkdir -p /export/apps/bbmap/38.67
$ sudo cp -r bbmap/* /export/apps/bbmap/38.67
bbmap-software.txt · Last modified: 2020/04/23 10:34 by aorth