sequencing depth vs quality assembly

Question

[v.shapovalova1]

Hello,

I have paired-end Illumina reads, now the depth of sequencing is 100x and I've found the plasmid consisted of one full-length contig. I'd like to check if depth 50x is good enough for my aims. How could I do it?

A lot of thanks, Valery

[JC]

what are your aims? just the assembly?

[v.shapovalova1]

Yes. I'd like to check the assembly with lower amount of reads. But i suppose that the indexes from forward and reverse should be the same. like in this post: Selecting Random Pairs From Fastq?

Answer 1

[Mensur Dlakic]

khmer can do digital normalization to 50x, though 100x is not too crazy in terms of sequencing depth.

[v.shapovalova1]

Thank you very much! seems that it's what I'm looking for. am i right that it'll removereads with the same indexes from formard file and reverse file?

[Mensur Dlakic]

That is correct. Everything is explained in the protocol.