Deep Sequencing Resources and User Information

We recommend eligible users get an account on the Green High Performance Computing Cluster for data delivery. To get an account, contact the UMassMed Help Desk at 856 - 8643, email them at, or request access through this form.

Alternatives for non-UMass customers are to have the data uploaded to an outside server (using SFTP) or transferred to an external drive meeting our requirements and shipped overnight.

Our current GHPCC data delivery system
(note this changes as resources improve/upgrade, so stay tuned):

    • Your lab or working group will have a directory at /nearline/deepseq/
    • You will get an email notification when your data files are ready.
    • If you require anything besides the Bustard output (includes fastq file)
      you must let us know at the time you submit your sample.
    • Data files will be deleted 5 business days after notification; please
      backup/copy/archive your data in your own workspace.
    • Data archive and recovery services are offered at an hourly fee. The
      DSCL must receive the archive request before the above-mentioned 5
      days are up.
  • You can find a Guide for UNIX and many other UMass Bioinformatics resources at
  • For a link to BioTools for Next Gen Sequencing Documents, click here.
  • The WIKI for the GHPCC is at
  • For information about NextGen BioInformatics Tools on GHPCC, click here. Please note that this list references the old HPCC, and some tools may no longer be available.
  • A handy calculator tool for DNA and RNA: NEBioCalculator
  • For a tool for Data Quality Score Viewing: FASTQC
  • Protocols and sample submission information are available on the Services page. Please click the Services link in the navigation panel for more information.
  • Technical Bulletins, Analytical tools, and BioInformatics information are being collected and posted on the DeepSeq Data Page.
  • Publications and information about deep/massively-parallel sequencing (MPSS) can be found on the Publications page at Illumina. We recommend starting with the review by DR Bentley, "Whole-genome re-sequencing".
  • The NIH Gene Expression Omnibus accepts Next Generation or Deep Sequencing data. Information about data submission and links to the tools at GEO may be found on the GEO Page.
  • We are establishing a library of reference genomes and analysis tools; we welcome requests and suggestions at

~ Nemo and Crew

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