bowtie.py¶

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 [FWD_READS [FWD_READS ...]]
                        </path/to/forward-reads.fastq>
  -2 [REV_READS [REV_READS ...]], --rev-reads [REV_READS [REV_READS ...]]
                        </path/to/reverse-reads.fastq>
  -U [SE_READS [SE_READS ...]], --se-reads [SE_READS [SE_READS ...]]
                        </path/to/single-end-reads.fastq>
  --cpus CPUS           Num processors to use.