CENTRIFUGE-INSPECT

NAME

centrifuge-inspect - inspecting the centrifuge index

SYNOPSIS

centrifuge-inspect [options]* <cf_base>

DESCRIPTION

Centrifuge version 1.0.3-beta by Daehwan Kim (infphilo@gmail.com, 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

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.