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