NAME

parse blast report and compute statistics on taxonomic affiliation

USAGE

blastx-parsing <infiles> [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input blast file [repeatable argument].

OPTIONS

--taxdir=<string>

path to the taxonomy directory [default: string.default].

--contam-list'=<string>

List of contaminant Taxa to compute stat [default: string.default].

--blast-extension=<string>

Specifia the extension of blast report file, the fasta file and the blast report must be the same out of extension [default: string.default].

--fasta-extension=<string>

Specifia the extension of blast report file, the fasta file and the blast report must be the same out of extension [default: string.default].

--length=<string>

minmal length of alignment to be considered for define bistcore [default: string.default].

--identity=<string>

minimal percentage of identity of alignment to be considered for define bistcore [default: string.default].

--bitscore=<string>

minimal percentage of bitscore for a hit to be considered for LCA [default: string.default].

--min-hit=<string>

minimal number of hit for a read to compute LCA [default: string.default].

--query-org=<string>

Name of Taxa of interest, supposed to be [default: string.default].