[mira_talk] FW: Higher contig numbers with MIRA 4 respect to MIRA 3.9.X
- From: "skizzo... ." <uomoazione@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 20 Mar 2014 10:13:00 +0000
Dear all,we sequence many bacteria with out IonTorrent and we are having
problems assembling IonTorrent bacterial data with the new MIRA 4.
An example: when two different datasets were assembled with MIRA 3.9.15 we got
73 and 48 contigs while when assembling the same two datasets with MIRA 4 we
got 373 and 206 contigs.
We used exactly the same settings and by MAUVE alignments the MIRA 4 assemblies
appear just far more fragmented. Reassembly of the assembled contigs helps a
lot but is not the best option obiously.
Our data is good (50X and 113X coverage for the two sequencing datasets i
mentioned) but assemblies with MIRA 4 are just too much fragmented!
For now we are still using MIRA 3.9.x but we're in search of an explanation :)
Thanks for the good work with MIRA, it is the BEST assembly software!
Andrea
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