What is the minimum required overlap to form a contig?

Theory behind mothur
1

The segment I’m sequencing is 529 bases long, while my resultant sequencing paired-end reads are 300 bases each. Will this be enough of an overlap to form a contig in mothur?
Thanks.

2

Hi Maria - I strongly discourage this strategy. You really need both reads to fully overlap with each other to get adequate denoising of the data. Also, the 2x300 chemistry is pretty bad for things like 16S rRNA gene sequences. You can see an old blog post that I wrote and is still relevant here…

Thanks,
Pat

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Thank you… so what would you suggest for an amplicon that’s 529 bp in length?

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Hi Maria - I would suggest generating phylotypes as described in the MiSeq SOP

Pat

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