twopaco - build the compacted de Bruijn graph from many complete
genomes
USAGE:
- twopaco
- {-f <integer>|--filtermemory <float>} [-o <file name>]
[--test] [--tmpdir <directory name>] [-a <integer>] [-t
<integer>] [-r <integer>] [-q <integer>] [-k
<oddc>] [--] [--version] [-h] <fasta files with genomes>
...
Where:
-f <integer>, --filtersize
<integer>
- (OR required)
- Size of the filter
-- OR --
--filtermemory <float>
- (OR required)
- Memory in GBs allocated for the filter
-o <file name>, --outfile <file
name>
- Output file name prefix
--test
- Run tests
--tmpdir <directory name>
- Temporary directory name
-a <integer>, --abundance
<integer>
- Vertex abundance threshold
-t <integer>, --threads <integer>
- Number of worker threads
-r <integer>, --rounds <integer>
- Number of computation rounds
-q <integer>, --hashfnumber
<integer>
- Number of hash functions
-k <oddc>, --kvalue <oddc>
- Value of k
--, --ignore_rest
- Ignores the rest of the labeled arguments following this flag.
--version
- Displays version information and exits.
-h, --help
- Displays usage information and exits.
- <fasta files with genomes>
- (accepted multiple times)
- (required)
- FASTA file(s) with nucleotide sequences.
- Program for construction of the condensed de Bruijn graph from complete
genomes
This manpage was written by Andrius Merkys for the Debian
distribution and
can be used for any other usage of the program.