Hi there,I am trying to benchmark Vicuna for HIV and HCV assembly. However, Vicuna typically generates hundreds of contigs in real datasets. Is this to be expected?
Am I correct in saying that the contig.fasta file should contain a single consensus sequence if all goes well?
Even when assembling simulated low error clonal HIV reads (100x reads generated by MASON with default 454 error profile, run through fakePairedReads.pl), Vicuna outputs 22 contigs. Other assemblers I have tested easily build a single contig from this dataset.
I am using default settings, specifying only input and output files.I feel I must be missing something obvious. What could I be doing wrong? Is Vicuna's performance dramatically improved by supplying paired end read data?
--Linked below are the simulated HBX2 reads to which I've referred in case they are of any interest.Many thanks,Bede Constantinides
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