Question: sequencing depth vs quality assembly
0
gravatar for v.shapovalova1
5 days ago by
v.shapovalova10 wrote:

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

quality assembly • 68 views
ADD COMMENTlink modified 5 days ago by Mensur Dlakic5.4k • written 5 days ago by v.shapovalova10

what are your aims? just the assembly?

ADD REPLYlink written 5 days ago by JC10k

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?

ADD REPLYlink written 4 days ago by v.shapovalova10
1
gravatar for Mensur Dlakic
5 days ago by
Mensur Dlakic5.4k
USA
Mensur Dlakic5.4k wrote:

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

ADD COMMENTlink written 5 days ago by Mensur Dlakic5.4k

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?

ADD REPLYlink written 4 days ago by v.shapovalova10

That is correct. Everything is explained in the protocol.

ADD REPLYlink written 4 days ago by Mensur Dlakic5.4k
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