gatb.core-API-1.3.0
Software dbgh5

Purpose of dbgh5

The dbgh5 binary creates a De Bruijn graph from an input bank (likely reads).

The output graph is saved in a HDF5 file. Such a file can be read through the gatb::core API by other tools. A classical workflow is the following:

Transfo.png
From reads to HDF5

Availability

dbgh5 is provided in the gatb::core distribution (see download page). You can get directly a binary or you can also compile it by yourself.

General algorithm

dbgh5 does all or part of the following steps:

  • counts the kmers of the input bank
  • put these kmers into a Bloom filter
  • compute an additional structure called cFP (for critical false positives)
  • locate some specific nodes in the De Bruijn graph

After these steps, one has a HDF5 file that holds the De Bruijn graph information. It can be then read through the gatb::core API.


Options

dbgh5 is highly configurable; the minimal requirement is the input set of reads, so you can just type for instance:

dbgh5 -in /somewhere/myreads.fasta

you can just type 'dbgh5' and you will get all the available options.

[graph options]
[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 '3']
-abundance-max (1 arg) : max abundance threshold for solid kmers [default '4294967295']
-histo-max (1 arg) : max number of values in kmers histogram [default '10000']
-solidity-kind (1 arg) : way to compute solids (sum, min or max) [default 'sum']
-solid-kmers-out (1 arg) : output file for solid kmers [default '']
-out (1 arg) : output file [default '']
-out-dir (1 arg) : output directory [default '.']
-minimizer-type (1 arg) : minimizer type (0=lexi, 1=freq) [default '0']
-minimizer-size (1 arg) : size of a minimizer [default '8']
[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]
-nb-cores (1 arg) : number of cores [default '0']
-max-disk (1 arg) : max disk (in MBytes) [default '0']
-max-memory (1 arg) : max memory (in MBytes) [default '2000']
-verbose (1 arg) : verbosity level [default '1']
-email (1 arg) : send statistics to the given email address [default '']
-email-fmt (1 arg) : 'raw' or 'xml' [default 'raw']