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  • #16
    I have moved to trimmomatic - it does SE and PE as well and in my hands much much faster.

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    • #17
      Originally posted by kga1978 View Post
      I have moved to trimmomatic - it does SE and PE as well and in my hands much much faster.
      FAR does SE/PE as well (starting from version 2 AFAIK).
      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?

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      • #18
        ea-utils is really fast, unfortunately lacks proper documentation

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        • #19
          Originally posted by dawe View Post
          ea-utils is really fast, unfortunately lacks proper documentation
          Yes, parameters and/or working principles are poorly documented. I agree, it is really fast.
          Are you using fastq-mcf in production?

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          • #20
            Originally posted by sklages View Post
            Yes, parameters and/or working principles are poorly documented. I agree, it is really fast.
            Are you using fastq-mcf in production?
            I'm using fastq-join and fastq-mcf. The first for overlapping paired end reads, the second to de-multiplex NuGEN RNA-seq libraries.
            I'm trying to get some more doc (the developer is very active...)

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