Pacbio Ccs Vs Subreads Explained ?

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10.5 years ago

curious.genome ▴ 40

Hi guys,

I've been trying to understand PacBio data for a while now, I think that it's the way forward for our lab. I'm still having trouble understanding CCS though - my biology is quite shaky.

Could someone explain to a computer scientist - how does PacBio get its CCS from the subreads or long reads ?
Our collaborators with the PacBio data gave us a set of files - with subreads.fastq, CCS.fastq and long_reads.fastq. When I ran a FASTQC report for subreads, I got base quality scores of around 10-15, whereas with CCS I got a larger variation for quality scores with values between 30-40. Is this expected ?
Which of these files should I use to perform assembly ? I'm guessing it's CCS.fastq

Thanks for your help!

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ADD COMMENT • link updated 10.0 years ago by Biostar 20 • written 10.5 years ago by curious.genome ▴ 40

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You asked the same question at seqanswers, where it was answered nicely. See http://seqanswers.com/forums/showthread.php?t=34790

ADD REPLY • link 10.5 years ago by lexnederbragt ★ 1.3k

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Question was helpful. Thank you.

ADD REPLY • link 10.0 years ago by Prakki Rama ★ 2.7k

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