Comments (1)
Hello,
I am currently working on this issue and contig ordering in the input fasta file has indeed impact on final results such as different number of contigs assigned to the same cluster as the contig assignment to plasmid clusters is iterative and order of contigs matters. The simplest solution is indeed resolve ties by an alphabetical ordering but this rather a simplistic solution
but would not necessarily capitalize on optimal (i.e. "correctness") of the final reconstructed plasmid. Instead we are testing now trying to order input contigs by lengths (from longest to shortest) before contig assignment to clusters. Sorry for delay as I was on vacation and it took some time to figure out the assign_contigs_to_clusters
logic and write unit test functions for testing and debugging.
from mob-suite.
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from mob-suite.