Closed chklopp closed 2 years ago
For repeated genomes such as Zea mays, the dgenies scaffolding procedure does not generate a correct output. Contigs are in the correct order but have often wrongly orientation.
To Reproduce You can reproduce the problem using the following files alignment.paf Zm-B73-REFERENCE-NAM-5.0.idx ZmWGA05a-01.bp.p_ctg.gfa.idx
Expected behavior All contigs should be oriented as the reference.
Screenshots example
For repeated genomes such as Zea mays, the dgenies scaffolding procedure does not generate a correct output. Contigs are in the correct order but have often wrongly orientation.
To Reproduce You can reproduce the problem using the following files alignment.paf Zm-B73-REFERENCE-NAM-5.0.idx ZmWGA05a-01.bp.p_ctg.gfa.idx
Expected behavior All contigs should be oriented as the reference.
Screenshots example