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 ...]
</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.