===========
coverage.py
===========

.. code-block:: bash

	usage: coverage.py

	Construct contig coverage table given an input `assembly` and provided files.
	Provided files may include one from the list below:
	1. `fwd_reads` and/or `rev_reads` and/or `se_reads`
	2. `sam` - alignment of `assembly` and `reads` in SAM format
	3. `bam` - alignment of `assembly` and `reads` in BAM format
	4. `bed` - alignment of `assembly` and `reads` in BED format

	optional arguments:
	  -h, --help            show this help message and exit
	  -f ASSEMBLY, --assembly ASSEMBLY
	                        </path/to/metagenome.fasta>
	  -1 [FWD_READS ...], --fwd-reads [FWD_READS ...]
	                        </path/to/forwards-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>
	  --sam SAM             </path/to/alignments.sam>
	  --bam BAM             </path/to/alignments.bam>
	  --bed BED             </path/to/alignments.bed>
	  --cpus CPUS           Num processors to use. (default: 2)
	  --from-spades         Extract k-mer coverages from contig IDs. (Input
	                        assembly is output from SPAdes)
	  --out OUT             Path to write a table of coverages