map2cov

Usage

usage: blobtools map2cov         -i FASTA [-b BAM...] [-a CAS...] [-s SAM...]
                                    [-o PREFIX] [--no_base_cov]
                                    [-h|--help]

    Options:
        -h --help                   show this
        -i, --infile FASTA          FASTA file of assembly. Headers are split at whitespaces.
        -b, --bam <BAM>...          BAM file (requires samtools in $PATH)
        -a, --cas <CAS>...          CAS file (requires clc_mapping_info in $PATH)
        -s, --sam <SAM>...          SAM file
        -o, --output <PREFIX>       Output prefix
        --no_base_cov               only parse read coverage (faster, but ...
                                        can only be used for "blobtools blobplot --noblobs")