Thursday, 11 November 2010

Bioscope 1.3 is a whopping 6.6 Gb!! Officially released for download

Downloading v 1.3 now. Gosh it is a whopping 6.6 Gb download.(270 Mb for v 1.21)
Not sure where the bloat comes from. Guessing it's example data, hope the server doesn't crash under the load. 
btw reason no. 5 for using Bioscope v 1.3 sounds quite flaky...

UPDATE: Argh. the md5sums match my download but I got this error
error []:  start of central directory not found;
  zipfile corrupt.
  (please check that you have transferred or created the zipfile in the
  appropriate BINARY mode and that you have compiled UnZip properly)

UPDATE2: Finally unzipped the 6.6 Gb file in an xp box using 7zip (apparently linux zip is finicky for files > 4 Gb. )
Guess what's inside? tarred zip files. Oh what fun to transfer them back to a linux box!
BioScope-1.3-9.tar.gz           (Regular, application/x-compressed-tar) size 217743781  mode 0744
BioScope-1.3.rBS130-51653_20101021190735.examples.tar.gz                (Regular, application/x-compressed-tar) size 4206422209 mode 0744
BS130-resources.tar.gz          (Regular, application/x-compressed-tar) size 2632156337 mode 0744

ABI has updated the downloads to a more reasonable 
208Mb Nov 25 04:24 bioscope1.3.1installer_4464106.tar.gz
md5 checksum is b688a8ae7b620d7b2dc7f68c6ca41783
Dear Valued Customer,

It is with great pleasure and excitement that I announce the release and immediate availability of BioScope v1.3

BioScope, the modular SOLiD™ data analysis bioinformatics tool, is designed specifically to optimize the accuracy of your SOLiD™ colorspace data.  In addition to streamlining the construction and maintenance of your SOLiD™ pipelines, BioScope provides a simple web interface allowing non command line users the power of running sophisticated NGS data analysis.

SOLiD™ BioScope provides workflow applications including:
  • Improved MaxMapper Mapping and Pairing
  • BFAST integration
  • Improved SAET Accuracy Enhancement
  • Resequencing Pipelines
    • SNP/diBayes
    • Inversion
    • CNV
    • Small Indel
    • Large Indel
  • Whole Transcriptome
  • Fusion Transcript and Splicing Detection
  • Target Resequencing
  • Support for ChIPSeq
  • Support for Methyl Miner
  • Annotation and Reporting
  • Improved BAM file compatibility
  • Improved BioScope™ Users Guide

Additional details can be found at the following blog:

Also attached is an in-depth article about our new Target Resequencing pipeline in BioScope™.

Please coordinate with your IT admin, bioinformatician, lab manager, and PI to have BioScope v1.3 installed at your site.

To get your free copy of SOLiDBioScope please go to:

Please ensure that you have an activated account on before downloading.  If you have problems downloading, please contact

If this is your first time installing BioScope, we strongly recommend working with the BioScope software installation team to ensure a proper installation and configuration of BioScope.  Please contact to inquire about our free BioScope software installation services.

For information BioScope training please contact your local bioinformatics FAS or go to


  1. So after going through this nightmare.... does anything work ? Was it worth the pain ? Or did you have to quit midway ?

    Sorry for my "intrusive" questions, but I'm
    trying to decide if to follow in your path, or just buy a proven, trivial to install commercial software like ISAS.


  2. Well, it seems improper for me to comment as I have no experience nor knowledge of what ISAS is. Would you care to elaborate on your experience?


Datanami, Woe be me