Degenerate graph constructed

[Pigrenok]

Hello!

I am trying to construct a graph using two very simple (artificial) sequences for testing purposes.

I tried several different cases (two sequences cases each): 1) - A-B-C

• A-D-C (middle block is substituted by another block, files seq{1,2}_2_substitution_mid.fa) 2) - A-B-C
  • A---C (middle block is deleted, files seq{1,2}_2_mid_block_indel.fa) where A, B, C and D are randomly generated 3000 bp sequences.

I tried to run it with all parameters at default as well as tried to vary some of the parameters. I attached the resulting GFA files for case 1 (substitute of the middle block). The same result is for case 2.

The following commands were used for default and one case of specific parameter values:

minigraph -x ggs -t 16 ./seqFile_2_substitution_mid.files/seq1_2_substitution_mid.fa ./seqFile_2_substitution_mid.files/seq2_2_substitution_mid.fa > ./out/test2.gfa

minigraph -x ggs -L 10 -l 100 -d 100 -q 1 -k 15 -q 10 -K 10k -t 16 ./seqFile_2_substitution_mid.files/seq1_2_substitution_mid.fa ./seqFile_2_substitution_mid.files/seq2_2_substitution_mid.fa > ./out/test.gfa

The file minigraphGithubIssue.zip contains all mentioned files.

Is it something that I do not understand or do something wrong? Or is it a glitch of minigraph?

By the way, is there a way to also get Paths in resulting GFA? Or it can only be done through separate alignment later (through converting GAF file separately?

Thank you very much in advance.

[lh3]

Is it something that I do not understand or do something wrong?

What is the exact problem?

Or it can only be done through separate alignment later (through converting GAF file separately?

That is the only way.