Hi all, I have a question regarding the --highlyrepetitive flag in mira 3.4.1.1 in paired-end 454 data. When I compare a whole BAC assembly with and wothout the --highlyrepetitive flag I get the attached picture. The X axis is the result of the following parameters: --job=denovo,genome,accurate,454 454_SETTINGS -LR:lsd=yes:ft=fastq -DP:ure=yes -CL:qc=yes -ED:ace=yes and the Y axis is the result of adding the --highlyrepetitive flag. The assemblies are quite similar, but for some reason there is one huge missassembly in the first reference contig. The mira manual does not say much about the flag and I wanted to know what are the exact changes of this flag in the assembly process. It is supposed to be a genomic region with multiple gene tandem duplications, so I thought this flag would help, but actually it has me a little puzzled. Which assembly do you think has the most accurate result? In the end I may have to do some Sanger sequencing myself for checking, but I was hoping to avoid it. Best regards, Juan Montenegro
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