.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.1.
.TH CENTRIFUGE-INSPECT "1" "October 2021" "centrifuge-inspect 1.0.3" "User Commands"
.SH NAME
centrifuge-inspect \- inspecting the centrifuge index
.SH SYNOPSIS
.B centrifuge-inspect
[\fI\,options\/\fR]\fI\,* <cf_base>\/\fR
.SH DESCRIPTION
Centrifuge version 1.0.3\-beta by Daehwan Kim (infphilo@gmail.com, http://www.ccb.jhu.edu/people/infphilo)
.TP
<cf_base>
cf filename minus trailing .1.cf/.2.cf/.3.cf
.IP
By default, prints FASTA records of the indexed nucleotide sequences to
standard out.  With \fB\-n\fR, just prints names.  With \fB\-s\fR, just prints a summary of
the index parameters and sequences.  With \fB\-e\fR, preserves colors if applicable.
.SH OPTIONS
.TP
\fB\-\-large\-index\fR
force inspection of the 'large' index, even if a
\&'small' one is present.
.TP
\fB\-a\fR/\-\-across <int>
Number of characters across in FASTA output (default: 60)
.TP
\fB\-n\fR/\-\-names
Print reference sequence names only
.TP
\fB\-s\fR/\-\-summary
Print summary incl. ref names, lengths, index properties
.TP
\fB\-e\fR/\-\-bt2\-ref
Reconstruct reference from .cf (slow, preserves colors)
.HP
\fB\-\-conversion\-table\fR Print conversion table
.TP
\fB\-\-taxonomy\-tree\fR
Print taxonomy tree
.TP
\fB\-\-name\-table\fR
Print names corresponding to taxonomic IDs
.TP
\fB\-\-size\-table\fR
Print the lengths of the sequences belonging to the same taxonomic ID
.TP
\fB\-v\fR/\-\-verbose
Verbose output (for debugging)
.TP
\fB\-h\fR/\-\-help
print detailed description of tool and its options
.TP
\fB\-\-help\fR
print this usage message
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.