Entering edit mode
4.4 years ago
alebesc
•
0
Hi there, I have MiSeq R1 and R2 libraries from four different BAC clones. I need to assemble their respective contigs using a genome reference assembly of Sea Urchins. I don't really know how to start this project. I was thinking on using a bwa pipeline but I am not sure if that is the most convenient way to obtain four contigs. I will appreciate any advise.
Thanks so much.
bwa
is an aligner so while it can be used to align your reads to urchin genome, it can't be used to assemble them. It would be worth aligning the reads to make sure they are from a region of the genome you are interested in before going on to assemblies.If you want to assemble your data you should probably start with
SPAdes
. Information about how to use SPAdes is available here.Edit: Hopefully you have 4 separate datasets corresponding to the 4 BAC's.
Yes I do have four separate datasets corresponding to each BAC Thanks!