coverage

Calculate coverage of sequences.

Produces coverage profiles for all sequences within a set of genome bins. This command requires sorted and indexed BAM files (i.e. a .bai index file must be present for each BAM file) produced with a tool such as BWA. Coverage profiles are required by the profile command and can be added to the extended qa table (qa -o 2 -c; see qa).

Arguments

usage: checkm coverage [-h] [-x EXTENSION] [-r] [-a MIN_ALIGN] [-e MAX_EDIT_DIST] [-m MIN_QC]
                       [-t THREADS] [-q]
                       bin_input output_file bam_files [bam_files ...]

Calculate coverage of sequences.

positional arguments:
  bin_input             directory containing bins (fasta format) or path to file describing genomes/genes - tab separated in 2 or 3 columns [genome ID, genome fna, genome translation file (pep)]
  output_file           print results to file
  bam_files             BAM files to parse

options:
  -h, --help            show this help message and exit
  -x, --extension EXTENSION
                        extension of bins (other files in directory are ignored) (default: fna)
  -r, --all_reads       use all reads to estimate coverage instead of just those in proper pairs
  -a, --min_align MIN_ALIGN
                        minimum alignment length as percentage of read length (default: 0.98)
  -e, --max_edit_dist MAX_EDIT_DIST
                        maximum edit distance as percentage of read length (default: 0.02)
  -m, --min_qc MIN_QC   minimum quality score (in phred) (default: 15)
  -t, --threads THREADS
                        number of threads (default: 1)
  -q, --quiet           suppress console output

Example: checkm coverage ./bins coverage.tsv example_1.bam example_2.bam

Example

checkm coverage ./bins coverage.tsv example_1.bam example_2.bam