Currently no idea of how diverse this repository is.
We have ~600bp PCR fragments containing 3 variable regions of roughly 30,30
and 60 bases.
For each pool we have 7.5mio reads (3.8mio pairs) and 6.8mio reads (3.4mio
pairs).
Concerning the IUPAC, I found fnicpst in the manual (now it called fnic, as
contig_consensus.C indicates)
2016-09-19 14:00 GMT+02:00 Bastien Chevreux <bach@xxxxxxxxxxxx>:
On 19 Sep 2016, at 4:32 , Sven Klages <sir.svencelot@xxxxxxxxx> wrote:
I have a pool of amplified antibody sequences (~600bp, pe100 illumina
data). All these sequences are extremely similar by nature.
"How similar?” would be my first question.
I want to assemble these fragments, so that every potential ab sequence
builds its own contig, avoiding (or trying to avoid) any IUPAC in the final
consensus.
Final contig set should represent the ab input pool / diversity.
Singlets will be removed in final dataset ..
What’s the amount of data you have? Coverage per amplcon / number of
amplicons?
B.
