bcalm - de Bruijn compaction in low memory

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

bcalm 2.2.1                                      September 2019                                         BCALM(1)

       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']

       bcalm - de Bruijn compaction in low memory