DOKK / manpages / debian 12 / gatb-core / dbgh5.1.en
DBGH5(1) User Commands DBGH5(1)

dbgh5 - builds a DeBruijn graph from a set of reads and save it as a HDF5 file

gatb-core-library

: 1.4.1
: 32 64 96 128

[graph options]

(0 arg) : don't construct the MPHF
[kmer count options]
(1 arg) : reads file
(1 arg) : size of a kmer [default '31']
(1 arg) : min abundance threshold for solid kmers [default '2']
(1 arg) : max abundance threshold for solid kmers [default '2147483647']
(1 arg) : min abundance hard threshold (only used when min abundance is "auto") [default '2']
(1 arg) : max number of values in kmers histogram [default '10000']
(1 arg) : way to compute counts of several files (sum, min, max, one, all, custom) [default 'sum']
(1 arg) : when solidity-kind is cutom, specifies list of files where kmer must be present [default '']
(1 arg) : max memory (in MBytes) [default '5000']
(1 arg) : max disk (in MBytes) [default '0']
(1 arg) : output file for solid kmers (only when constructing a graph) [default '']
(1 arg) : output file [default '']
(1 arg) : output directory [default '.']
(1 arg) : output directory for temporary files [default '.']
(1 arg) : h5 compression level (0:none, 9:best) [default '0']
(1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5']
[kmer count, algorithmic options options]
(1 arg) : minimizer type (0=lexi, 1=freq) [default '0']
(1 arg) : size of a minimizer [default '10']
minimizer repartition (0=unordered, 1=ordered) [default '0']
[bloom options]
(1 arg) : bloom type ('basic', 'cache', 'neighbor') [default 'neighbor']
(1 arg) : debloom type ('none', 'original' or 'cascading') [default 'cascading']
debloom impl ('basic', 'minimizer') [default 'minimizer']
[branching options]
branching type ('none' or 'stored') [default 'stored']
(1 arg) : topological information level (0 for none) [default '0']
[general options]
(0 arg) : dump config only
(1 arg) : number of cores [default '0']
(1 arg) : verbosity level [default '1']
integers precision (0 for optimized value) [default '0']
(1 arg) : send statistics to the given email address [default '']
(1 arg) : 'raw' or 'xml' [default 'raw']
(1 arg) : check result with previous result [default '']
(1 arg) : dump some properties of the created graph into a file [default '']
[debug
options]
debug function, redo the bcalm algo
same, but skip bcalm
same, but redo bglue
same, but skip bglue
same, but redo links
same, but skip links

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