=========
bowtie.py
=========

.. code-block:: bash

	usage: bowtie.py

	Align provided reads to metagenome `assembly` and write alignments to
	`sam`.NOTE: At least one reads file is required.

	positional arguments:
	  assembly              </path/to/assembly.fasta>
	  database              </path/to/alignment.database>. Will construct database
	                        at provided path if not found.
	  sam                   </path/to/alignment.sam>

	optional arguments:
	  -h, --help            show this help message and exit
	  -1 [FWD_READS ...], --fwd-reads [FWD_READS ...]
	                        </path/to/forward-reads.fastq>
	  -2 [REV_READS ...], --rev-reads [REV_READS ...]
	                        </path/to/reverse-reads.fastq>
	  -U [SE_READS ...], --se-reads [SE_READS ...]
	                        </path/to/single-end-reads.fastq>
	  --cpus CPUS           Num processors to use.