centrifuge-inspect(1)

Usage

centrifuge-inspect [options] * <cf_base>

Overview

Centrifuge version 1.0.3-beta by Daehwan Kim ([email protected], http://www.ccb.jhu.edu/people/infphilo)

<cf_base>: cf filename minus trailing .1.cf/.2.cf/.3.cf

: By default, prints FASTA records of the indexed nucleotide sequences to standard out. With -n, just prints names. With -s, just prints a summary of the index parameters and sequences. With -e, preserves colors if applicable.

Options

--large-index: force inspection of the 'large' index, even if a 'small' one is present.

`-a/--across <int>`	Number of characters across in FASTA output (default: 60)
`-n/--names`	Print reference sequence names only
`-s/--summary`	Print summary incl. ref names, lengths, index properties
`-e/--bt2-ref`	Reconstruct reference from .cf (slow, preserves colors)

--conversion-table Print conversion table

--taxonomy-tree: Print taxonomy tree

--name-table: Print names corresponding to taxonomic IDs

--size-table: Print the lengths of the sequences belonging to the same taxonomic ID

`-v/--verbose`	Verbose output (for debugging)
`-h/--help`	print detailed description of tool and its options

--help: print this usage message

Releases

4 releases since Debian 10 (Buster); the text changed 1 time.

--help since Debian 12 (Bookworm); --large-index since Debian 12 (Bookworm); --name-table since Debian 12 (Bookworm); --size-table since Debian 12 (Bookworm); --taxonomy-tree since Debian 12 (Bookworm).