====== 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: 38.67
  * Added: September, 2019
  * Link: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide

===== 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/38.67
$ 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 [[https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/|the documentation]] for more information.

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

<code>$ 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</code>