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 ...]
</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