.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH DBGH5 "1" "May 2018" "dbgh5 1.4.1" "User Commands"
.SH NAME
dbgh5 \- builds a DeBruijn graph from a set of reads and save it as a HDF5 file
.SH DESCRIPTION
gatb\-core\-library
.TP
version
: 1.4.1
.TP
build_kmer_size
: 32 64 96 128
.PP
[graph options]
.TP
\fB\-no\-mphf\fR
(0 arg) :    don't construct the MPHF
.IP
[kmer count options]
.TP
\fB\-in\fR
(1 arg) :    reads file
.TP
\fB\-kmer\-size\fR
(1 arg) :    size of a kmer  [default '31']
.TP
\fB\-abundance\-min\fR
(1 arg) :    min abundance threshold for solid kmers  [default '2']
.TP
\fB\-abundance\-max\fR
(1 arg) :    max abundance threshold for solid kmers  [default '2147483647']
.TP
\fB\-abundance\-min\-threshold\fR
(1 arg) :    min abundance hard threshold (only used when min abundance is "auto")  [default '2']
.TP
\fB\-histo\-max\fR
(1 arg) :    max number of values in kmers histogram  [default '10000']
.TP
\fB\-solidity\-kind\fR
(1 arg) :    way to compute counts of several files (sum, min, max, one, all, custom)  [default 'sum']
.TP
\fB\-solidity\-custom\fR
(1 arg) :    when solidity\-kind is cutom, specifies list of files where kmer must be present  [default '']
.TP
\fB\-max\-memory\fR
(1 arg) :    max memory (in MBytes)  [default '5000']
.TP
\fB\-max\-disk\fR
(1 arg) :    max disk   (in MBytes)  [default '0']
.TP
\fB\-solid\-kmers\-out\fR
(1 arg) :    output file for solid kmers (only when constructing a graph)  [default '']
.TP
\fB\-out\fR
(1 arg) :    output file  [default '']
.TP
\fB\-out\-dir\fR
(1 arg) :    output directory  [default '.']
.TP
\fB\-out\-tmp\fR
(1 arg) :    output directory for temporary files  [default '.']
.TP
\fB\-out\-compress\fR
(1 arg) :    h5 compression level (0:none, 9:best)  [default '0']
.TP
\fB\-storage\-type\fR
(1 arg) :    storage type of kmer counts ('hdf5' or 'file')  [default 'hdf5']
.IP
[kmer count, algorithmic options options]
.TP
\fB\-minimizer\-type\fR
(1 arg) :    minimizer type (0=lexi, 1=freq)  [default '0']
.TP
\fB\-minimizer\-size\fR
(1 arg) :    size of a minimizer  [default '10']
.TP
\fB\-repartition\-type\fR (1 arg) :
minimizer repartition (0=unordered, 1=ordered)  [default '0']
.IP
[bloom options]
.TP
\fB\-bloom\fR
(1 arg) :    bloom type ('basic', 'cache', 'neighbor')  [default 'neighbor']
.TP
\fB\-debloom\fR
(1 arg) :    debloom type ('none', 'original' or 'cascading')  [default 'cascading']
.TP
\fB\-debloom\-impl\fR (1 arg) :
debloom impl ('basic', 'minimizer')  [default 'minimizer']
.IP
[branching options]
.TP
\fB\-branching\-nodes\fR (1 arg) :
branching type ('none' or 'stored')  [default 'stored']
.TP
\fB\-topology\-stats\fR
(1 arg) :    topological information level (0 for none)  [default '0']
.IP
[general options]
.TP
\fB\-config\-only\fR
(0 arg) :    dump config only
.TP
\fB\-nb\-cores\fR
(1 arg) :    number of cores  [default '0']
.TP
\fB\-verbose\fR
(1 arg) :    verbosity level  [default '1']
.TP
\fB\-integer\-precision\fR (1 arg) :
integers precision (0 for optimized value)  [default '0']
.TP
\fB\-email\fR
(1 arg) :    send statistics to the given email address  [default '']
.TP
\fB\-email\-fmt\fR
(1 arg) :    'raw' or 'xml'  [default 'raw']
.TP
\fB\-check\fR
(1 arg) :    check result with previous result  [default '']
.TP
\fB\-check\-dump\fR
(1 arg) :    dump some properties of the created graph into a file  [default '']
.TP
[debug
options]
.TP
\fB\-redo\-bcalm\fR (0 arg) :
debug function, redo the bcalm algo
.TP
\fB\-skip\-bcalm\fR (0 arg) :
same, but       skip     bcalm
.TP
\fB\-redo\-bglue\fR (0 arg) :
same, but       redo     bglue
.TP
\fB\-skip\-bglue\fR (0 arg) :
same, but       skip     bglue
.TP
\fB\-redo\-links\fR (0 arg) :
same, but       redo     links
.TP
\fB\-skip\-links\fR (0 arg) :
same, but       skip     links
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.