I have ~100 genomes of fungi. They have been grouped based on their distance, itself based on their sequences.
Within each of 8 groups, I want to improve the contig assemblies by using the genomes of other members of the group as scaffolds. But I do not want sequence lift-over - just improved assembly of only one target genome at a time, using other genomes as multiple references.
MeDuSa does this, but I have a test run of just 1 target Vs 2 reference that has been going on for >8 hrs. So I am looking for alternatives that are less cpu / RAM hungry, and that scale-up well when each group has ~8-10 genomes. Anyone out there with experience in using alternatives like RagOut or Multi-CAR, or other multi-reference scaffolders I have not yet come across?
PS. Some assemblies I am using are very fragmented, and it's possible that is contributing to long run times. Nevertheless, if you've performed an apples-to-apples comparison, and know there is a better alternative to MeDuSa, please ping back
You can give Chromosomer a try - I can't say much about the run time though since it relies on alignments from maf-files converted to blast-tab