Lucy has been used here for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers.
Documentation is very sparse. For what exists, see:
Any pointers to additional documentation would be appreciated.
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