Hi all,
We are currently trying to design a pipeline for viral sequencing with Illumina. For the alignment, we were considering using Mosaik with an ambiguous reference sequence. This sequence is constructed from 80 downloaded sequences. We also constructed an unambiguous sequence from the same data.
Funnily enough, aligning with respect to the unambiguous reference sequence gave us decent alignment stats (% of reads mapped were in the 80-98 range), whereas alignment percentages using an ambiguous reference sequence were in the 14-41% range.
We are currently using the following parameters: -hs 11 -mmp 0.08. This is all done in Mosaik v2.1.73.
Does anyone know whether Mosaik v2 still supports IUPAC? Should we be using some flag that I'm unaware of? Is the hashsize too big to deal with IUPAC coded references? Any pointers are welcome. It's not that we're not happy with the current results -- we just want to *know...
Thanks for your help,
Elise
We are currently trying to design a pipeline for viral sequencing with Illumina. For the alignment, we were considering using Mosaik with an ambiguous reference sequence. This sequence is constructed from 80 downloaded sequences. We also constructed an unambiguous sequence from the same data.
Funnily enough, aligning with respect to the unambiguous reference sequence gave us decent alignment stats (% of reads mapped were in the 80-98 range), whereas alignment percentages using an ambiguous reference sequence were in the 14-41% range.
We are currently using the following parameters: -hs 11 -mmp 0.08. This is all done in Mosaik v2.1.73.
Does anyone know whether Mosaik v2 still supports IUPAC? Should we be using some flag that I'm unaware of? Is the hashsize too big to deal with IUPAC coded references? Any pointers are welcome. It's not that we're not happy with the current results -- we just want to *know...
Thanks for your help,
Elise
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