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Ho to assembly MiSeq reads from BAC clones into a contig in fasta format?

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.

assembly bac library next-gen sequencing
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updated by GenoMax GenoMax • written by alebesc • alebesc

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.

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written by GenoMax GenoMax

Yes I do have four separate datasets corresponding to each BAC Thanks!

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written by alebesc • alebesc

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