coverage.py¶

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 [FWD_READS [FWD_READS ...]]
                        </path/to/forwards-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>
  --sam SAM             </path/to/alignments.sam>
  --bam BAM             </path/to/alignments.bam>
  --lengths LENGTHS     Path to tab-delimited lengths table with columns of
                        contig & length.
  --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