Provided by: gatb-core_1.4.1+git20190813.a73b6dd+dfsg-1_amd64 bug

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.