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Constructs segment repeat-free founder block graphs from multiple sequence alignments

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founderblockgraphs

Constructs repeat-free/semi-repeat-free non-elastic/elastic founder graphs from multiple sequence alignments.

getting started

Clone this repository with dependencies:

$ git clone --recurse-submodules https://github.com/algbio/founderblockgraphs.git
$ cd founderblockgraphs

Build sdsl-lite-v3:

$ cd sdsl-lite-v3
$ ./install.sh .
$ cd ..

Build this project (founderblockgraph, locate_multiple, locate_patterns):

$ make

usage

Usage: founderblockgraph --input=MSA.fasta --output={MSA.index|efg.xgfa} [--gfa]
[--elastic] [--gap-limit=GAPLIMIT] [--threads=THREADNUM]
[--graphviz-output=efg.dot] [--output-paths] [--ignore-chars="ALPHABET"]
Constructs a semi-repeat-free (Elastic) Founder Graph

Input is MSA given in fasta format. In standard mode (without --elastic), rows
with runs of gaps ‘-’ or N’s ≥ GAPLIMIT will be filtered out.

  -h, --help                    Print help and exit
      --full-help               Print help, including hidden options, and exit
  -V, --version                 Print version and exit
      --input=filename          MSA input path
      --output=filename         Index/EFG output path
      --gap-limit=GAPLIMIT      Gap limit (suppressed by --elastic)
                                  (default=`1')
      --graphviz-output=filename
                                Graphviz output path
      --memory-chart-output=filename
                                Memory chart output path
  -e, --elastic                 Min-max-length semi-repeat-free segmentation
                                  (default=off)
      --gfa                     Saves output in xGFA format  (default=off)
  -p, --output-paths            Print the original sequences as paths of the
                                  xGFA graph (requires --gfa)  (default=off)
      --ignore-chars=STRING     Ignore these characters for the indexability
                                  property/pattern matching
  -t, --threads=THREADNUM       Max # threads  (default=`-1')

todo

  • document EFG tricks related to option --ignore-chars, to the start and end of sequences, and to initial and ending runs of gaps
  • implement validation of .gfa files
  • implement pattern matching (locate_multiple, locate_patterns) on EFGs
  • implement min max height segmentation

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Constructs segment repeat-free founder block graphs from multiple sequence alignments

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