table of contents
| DBGH5(1) | User Commands | DBGH5(1) |
NAME¶
dbgh5 - builds a DeBruijn graph from a set of reads and save it as a HDF5 file
DESCRIPTION¶
gatb-core-library
- version
- : 1.4.1
- build_kmer_size
- : 32 64 96 128
[graph options]
- -no-mphf
- (0 arg) : don't construct the MPHF
- [kmer count options]
- -in
- (1 arg) : reads file
- -kmer-size
- (1 arg) : size of a kmer [default '31']
- -abundance-min
- (1 arg) : min abundance threshold for solid kmers [default '2']
- -abundance-max
- (1 arg) : max abundance threshold for solid kmers [default '2147483647']
- -abundance-min-threshold
- (1 arg) : min abundance hard threshold (only used when min abundance is "auto") [default '2']
- -histo-max
- (1 arg) : max number of values in kmers histogram [default '10000']
- -solidity-kind
- (1 arg) : way to compute counts of several files (sum, min, max, one, all, custom) [default 'sum']
- -solidity-custom
- (1 arg) : when solidity-kind is cutom, specifies list of files where kmer must be present [default '']
- -max-memory
- (1 arg) : max memory (in MBytes) [default '5000']
- -max-disk
- (1 arg) : max disk (in MBytes) [default '0']
- -solid-kmers-out
- (1 arg) : output file for solid kmers (only when constructing a graph) [default '']
- -out
- (1 arg) : output file [default '']
- -out-dir
- (1 arg) : output directory [default '.']
- -out-tmp
- (1 arg) : output directory for temporary files [default '.']
- -out-compress
- (1 arg) : h5 compression level (0:none, 9:best) [default '0']
- -storage-type
- (1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5']
- [kmer count, algorithmic options options]
- -minimizer-type
- (1 arg) : minimizer type (0=lexi, 1=freq) [default '0']
- -minimizer-size
- (1 arg) : size of a minimizer [default '10']
- -repartition-type (1 arg) :
- minimizer repartition (0=unordered, 1=ordered) [default '0']
- [bloom options]
- -bloom
- (1 arg) : bloom type ('basic', 'cache', 'neighbor') [default 'neighbor']
- -debloom
- (1 arg) : debloom type ('none', 'original' or 'cascading') [default 'cascading']
- -debloom-impl (1 arg) :
- debloom impl ('basic', 'minimizer') [default 'minimizer']
- [branching options]
- -branching-nodes (1 arg) :
- branching type ('none' or 'stored') [default 'stored']
- -topology-stats
- (1 arg) : topological information level (0 for none) [default '0']
- [general options]
- -config-only
- (0 arg) : dump config only
- -nb-cores
- (1 arg) : number of cores [default '0']
- -verbose
- (1 arg) : verbosity level [default '1']
- -integer-precision (1 arg) :
- integers precision (0 for optimized value) [default '0']
- (1 arg) : send statistics to the given email address [default '']
- -email-fmt
- (1 arg) : 'raw' or 'xml' [default 'raw']
- -check
- (1 arg) : check result with previous result [default '']
- -check-dump
- (1 arg) : dump some properties of the created graph into a file [default '']
- [debug
- options]
- -redo-bcalm (0 arg) :
- debug function, redo the bcalm algo
- -skip-bcalm (0 arg) :
- same, but skip bcalm
- -redo-bglue (0 arg) :
- same, but redo bglue
- -skip-bglue (0 arg) :
- same, but skip bglue
- -redo-links (0 arg) :
- same, but redo links
- -skip-links (0 arg) :
- same, but skip links
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
| May 2018 | dbgh5 1.4.1 |