====== 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 =====

  * Version: 38.95
  * Added: September, 2019
  * Updated: February, 2022
  * Link: https://sourceforge.net/projects/bbmap/
===== Usage =====

See versions of bbmap which are available:
<code>$ module avail bbmap</code>

Load one version into your environment and run it:
<code>$ module load bbmap/38.95
$ bbmap.sh</code>

**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 ''bbmap.sh -h'' for more information.

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ tar xf BBMap_38.95.tar.gz
$ wget https://liquidtelecom.dl.sourceforge.net/project/bbmap/BBMap_38.95.tar.gz
$ sudo mkdir -p /export/apps/bbmap/38.95
$ sudo cp -r bbmap/* /export/apps/bbmap/38.95</code>