Question

sequencing depth vs quality assembly

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4.5 years ago

v.shapovalova1 ▴ 10

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

Assembly quality • 1.1k views

ADD COMMENT • link updated 4.5 years ago by Mensur Dlakic ★ 28k • written 4.5 years ago by v.shapovalova1 ▴ 10

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what are your aims? just the assembly?

ADD REPLY • link 4.5 years ago by JC 13k

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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 REPLY • link 4.5 years ago by v.shapovalova1 ▴ 10

score 1 · Answer 1 · 2020-05-22

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4.5 years ago

Mensur Dlakic ★ 28k

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

ADD COMMENT • link 4.5 years ago by Mensur Dlakic ★ 28k

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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?