create

Usage

usage: blobtools create     -i FASTA [-y FASTATYPE] [-o PREFIX] [--title TITLE]
                              [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...]
                              [--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>]
                              [-t HITS...] [-x TAXRULE...] [-m FLOAT] [-d FLOAT] [--tax_collision_random]
                              [-h|--help]

    Options:
        -h --help                       show this
        -i, --infile FASTA              FASTA file of assembly. Headers are split at whitespaces.
        -y, --type FASTATYPE            Assembly program used to create FASTA. If specified,
                                        coverage will be parsed from FASTA header.
                                        (Parsing supported for 'spades', 'velvet', 'platanus')
        -t, --hitsfile HITS...          Hits file in format (qseqid\ttaxid\tbitscore)
                                        (e.g. BLAST output "--outfmt '6 qseqid staxids bitscore'")
                                        Can be specified multiple times
        -x, --taxrule <TAXRULE>...      Taxrule determines how taxonomy of blobs
                                        is computed (by default both are calculated)
                                        "bestsum"       : sum bitscore across all
                                                          hits for each taxonomic rank
                                        "bestsumorder"  : sum bitscore across all
                                                          hits for each taxonomic rank.
                                                  - If first <TAX> file supplies hits, bestsum is calculated.
                                                  - If no hit is found, the next <TAX> file is used.
        -m, --min_score <FLOAT>         Minimal score necessary to be considered for taxonomy calculaton, otherwise set to 'no-hit'
                                        [default: 0.0]
        -d, --min_diff <FLOAT>          Minimal score difference between highest scoring
                                        taxonomies (otherwise "unresolved") [default: 0.0]
        --tax_collision_random          Random allocation of taxonomy if highest scoring
                                        taxonomies have equal scores (otherwise "unresolved") [default: False]
        --nodes <NODES>                 NCBI nodes.dmp file. Not required if '--db'
        --names <NAMES>                 NCBI names.dmp file. Not required if '--db'
        --db <NODESDB>                  NodesDB file (default: $BLOBTOOLS/data/nodesDB.txt).
        -b, --bam <BAM>...              BAM file(s), can be specified multiple times
        -s, --sam <SAM>...              SAM file(s), can be specified multiple times
        -a, --cas <CAS>...              CAS file(s) (requires clc_mapping_info in $PATH), can be specified multiple times
        -c, --cov <COV>...              COV file(s), can be specified multiple times
        -o, --out <PREFIX>              BlobDB output prefix
        --title TITLE                   Title of BlobDB [default: output prefix)

Comments

• Input files
• one assembly file, e.g. example/assembly.fna
• one (or more) coverage file(s), e.g. example/mapping_1.bam
• one (or more) hits file(s), e.g. example/blast.out