NAME
centrifuge-inspect - inspecting the centrifuge index
SYNOPSIS
centrifuge-inspect [options]* <cf_base>
DESCRIPTION
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
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.