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Graphite V2

Find longest maximum exact matches, LMEMS, in a collection of sequences

Graphite starts with two graph files (from Cuttlefish) and a set of query identifiers. It then builds a suffix array of the queries along with other datastructures to speed up matching. Then each sequence (i.e "reference") is read from the graph file and mapped onto the Suffix array. Each mapping is an identical sequence between the queries and ref, also called Maximum Exact Matches (MEMs). Each time a MEM is found its length is compared to previously discovered MEMs to only retain the Longest MEM (LMEM).

Usage

Make sure Julia is installed:

Run julia --version if the command is not found install Julia from here. Then go to the package manager by first starting julia (julia) and pressing ] then type: add ArgPrase and after that add OrdereCollections then you can leave julia (exit with Backspace and then typing exit())

Clone the repo git clone https://github.com/rickbeeloo/GraphiteV2 This already includes libasais but can then only be used from within the GraphiteV2 folder.

To use graphite:

julia main.jl -g test_data/phage_graph.cf_seq -s test_data/phage_graph.cf_seg -k 31 -o test_data/output.txt -q test_data/query.txt

  • -g, the graph path file, when constructed using Cuttlefish the .cf_seq file.
  • -s, the node sequence file, when constructed using Cuttlefish the .cf_seg file
  • -k, the k-mer size used to build the graph (i.e. 31 nucleotides)
  • -q, a file with query identifiers. These should match those in -g
  • -o, the output file path

To run with multiple threads add NUM_JULIA_THREADS=X before your command where X is the number of threads, for example: NUM_JULIA_THREADS=10 julia main.jl ..

Output

The output file looks like:

Reference:1_Sequence:MT952848.1	2	1	112	112
Reference:1_Sequence:MT952848.1	1	150	184	35
Reference:1_Sequence:MT952848.1	1	192	337	146
Reference:1_Sequence:MT952848.1	1	339	398	60
Reference:1_Sequence:MT952848.1	1	432	491	60

Which has five columns:

  1. The query identifier (as in -q)
  2. The reference index (1-based)
  3. The start position in nucleotides on the query sequence
  4. The end position in nucleotides on the query sequence
  5. The original MEM length*

So for example, Reference:1_Sequence:MT952848.1 matches the first 112 nucleotides with the second reference in the file (test_data/phage_graph.cf_seq)

*The original MEM size corresponding to the LMEM, to get the LMEM length use end-start+1

Citation

If you use Graphite in your research, please cite:

Rick Beeloo, Aldert L. Zomer, and Bas E. Dutilh. "Graphite: painting genomes using a colored De Bruijn graph". BioRXiv Preprint. DOI: 10.1101/2023.10.08.561343. https://www.biorxiv.org/content/10.1101/2023.10.08.561343v1.full