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,
what are your aims? just the assembly?
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?
khmer can do digital normalization to 50x, though 100x is not too crazy in terms of sequencing depth.
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?
That is correct. Everything is explained in the protocol.
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