I have moved to trimmomatic - it does SE and PE as well and in my hands much much faster.
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FAR does SE/PE as well (starting from version 2 AFAIK).Originally posted by kga1978 View Post
Speed is not really a matter for me. If it takes five minutes per lane, fine, if it takes one hour, fine too (considering instrument run time and time for downstream analysis) :-)
Have you compared the results? Similar?Comment
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Yes, parameters and/or working principles are poorly documented. I agree, it is really fast.Originally posted by dawe View Post
Are you using fastq-mcf in production?Comment
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I'm using fastq-join and fastq-mcf. The first for overlapping paired end reads, the second to de-multiplex NuGEN RNA-seq libraries.Originally posted by sklages View Post
I'm trying to get some more doc (the developer is very active...)Comment
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