MitoBim results
Hi there, I've been using mitobim1.8 to reconstruct mitochondrial genomes from a bird using a related species. It seems to have worked; however I don't quite understand the output. In my last iteration file, there are a number of padded and unpadded fasta files... named, for example: sample-reference-out- AllStrains.padded.fasta sample-reference-out- AllStrains.unpadded.fasta sample-reference-out-sample. padded.fasta sample-reference-out-sample. unpadded.fasta sample-reference-out- reference.padded.fasta sample-reference-out- reference.unpadded.fasta I understand the difference between the unpadded and padded, but not AllStrains vs sample vs reference. Could you please explain this to me? I think I've worked out that the AllStrains is being used as the backbone for the next iteration. However this confuses me, as it also appears that in the info folder from mira, in the assembly.txt file all the tags relate to the sample version. Also, I was wondering if you have