DBGH5

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’]

-email

(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.