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Roche FLX+ software update v. 2.9



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  • Roche FLX+ software update v. 2.9

    Hi there,

    Roche released a new version of its software for FLX+, you can read the announcement here:


    "The latest software enables sequencing of amplicons up to 800 bp while maintaining >99% accuracy over the length of the read."

    The sequencing company I use already tests this software, and they have sent me the results processed with the new version. I got fewer sequences, which is due to the fact that there are no sequences shorter than about 365 bp. So of course this results in higher average sequence length.

    Does anyone know if this cutoff is a built-in feature of the new version, or just something you can implement if you want?

  • #2
    Hello Krisztab,

    This is a feature built into software version 2.9. When processing long amplicons on the GS FLX+ platform, there are three signal processing options offering varying degrees of read filtering stringency. The first pipeline is the most similar to the current Amplicon pipeline, which is the most stringent and rejects reads of poorer quality. The other two pipelines are more similar to the shotgun pipeline and will trim back the poorer quality bases from reads rather than reject the entire read. These pipelines will also reject reads trimmed shorter than 700 flows (~390 base pairs) which can be recovered by changing the qualityMinLength filter and reprocessing or reprocessing with the shotgun pipeline.

    You may want to ask your sequencing provider to reprocess with the other pipelines to determine which is best suited for your needs.



    Nicole Whitney
    Senior Specialist
    Customer Support
    454 Life Sciences, A Roche Company


    • #3
      Hey Nicole,

      I am trying to find 2.9 upgrade from GS Jr, but cannot. Can you please point me in right direction?