NAME

       bcalm - de Bruijn compaction in low memory

DESCRIPTION

       Bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

       [bcalm_1 options]

       -nb-cores (1 arg) :
              number of cores  [default '0']

       -verbose
              (1 arg) :    verbosity level  [default '1']

       -version
              (0 arg) :    version

       -help  (0 arg) :    help

              [graph options]

       -no-mphf
              (0 arg) :    don't construct the MPHF

              [kmer count options]

       -in    (1 arg) :    reads file  [default '']

       -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']

       -solidity-custom
              (1  arg) :    when solidity-kind is custom, 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']

       -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']

       -histo2D
              (1 arg) :    compute the 2D histogram (with first file = genome, remaining files  =
              reads)  [default '0']

       -histo (1 arg) :    output the kmer abundance histogram  [default '0']

              [kmer count, advanced performance tweaks options]

       -minimizer-type
              (1 arg) :    minimizer type (0=lexi, 1=freq)  [default '1']

       -minimizer-size
              (1 arg) :    size of a minimizer  [default '10']

       -repartition-type (1 arg) :
              minimizer repartition (0=unordered, 1=ordered)  [default '1']

              [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']

       [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

       -nb-glue-partitions (1 arg) :
              number of glue partitions (automatically calculated by default)  [default '0']

AUTHOR

       This manpage was written by Shayan Doust for the Debian distribution and can be  used  for
       any other usage of the program.