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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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Generate HiFi reads #687

Closed mariachiara-github closed 1 month ago

mariachiara-github commented 2 months ago

Hi! What are the parameters to get HiFi reads? The minimum passes need to be at least 3 and the rq value of 0.99 ? Something like the code below should give me HiFi reads, is this correct ? $ccs7 --reportFile --minPasses=3 --minPredictedAccuracy=0.99 --logFile mylog.txt subreads.bam ccs.bam

P.S.: I'm using version 7.0 of SMRT Link tools, and version 3.4.1 of ccs (the samples I'm working with use an old chemistry, so I can't use the last version of ccs)

Thank you for the help!!

armintoepfer commented 1 month ago

HiFi means >=Q20. In your case, the configuration is correct.