Site Notices

Update June 1st : GenSAS site maintenance will occur between 8:00 AM and 12:00 PM PST. All running GenSAS jobs will continue to run during these down times.  We apologize for the inconvenience.

New Features and Updates

This page will document the differences between GenSAS versions and when GenSAS was last updated.

Version 6.0 (September 2018)

  • BRAKER can take multple BAM files (9/6/19)
  • Added option to upload aligned BAM file of previously aligned RNA-seq reads (12/15/18)
  • Protein sequence parsing problem fixed, added ability to run BUSCO at OGS step (10/16/18)
  • Addition of BUSCO, HISAT2, DIAMOND, pBLAT (version of BLAT that runs multi-threaded), BRAKER2
  • Option to use soft-masked sequence with some gene prediction tools added
  • Summary report of tools and setting used to generate OGS produced at Publish step
  • BLAT, BLAST+, InterProScan, HISAT2, DIAMOND, BRAKER2, GeneMark-ES, TopHat2, PASA now all run multi-threaded on the cluster
  • Assembly sequence names processed to remove special characters and for length
  • Option to make combined GFF3 file with OGS, repeats, rRNA, tRNA data and functional annotation info in column 9 added to Publish step

Version 5.1 (January 2018)

  • Upgraded to use Tomcat 8 and Apollo2
  • Added Help section to accordion menu
  • Implemented restrictions on user accounts 
  • Added PRINSEQ to check assembly quality at Sequence step
  • GenSAS jobs now sent to computational cluster
  • Gene models that were manually edited also have functional tools run on them during integration into OGS

Version 5.0 (January 2017)

  • Sequences step added before Project step to allow users to create subsets of sequences
  • Evidence step divided into GFF3 and Evidence steps
  • Align step added before structural annotation to allow TopHat alignments of RNA-seq data to be used to train Augustus
  • OGS (official gene set) step added
  • Illumina RNA-seq read upload added
  • GeneMarkS, GeneMarkES, RNAmmer added
  • User-created annotations from Apollo integrated into OGS during Publish step
  • User Manual added

Version 4.0 (2015-2016)

  • Reorganization of how data is stored to improve the parent-child relationships
  • Functional annotation tools added
  • Structural and functional annotation

Version 3.0 (2014-2015)

  • New single page interface design (current interface)
  • Integration of JBrowse and Apollo
  • Structural annotation only

Version 2.0 (2012-2014)

  • Removed the size limit on DNA sequences
  • Improved the user interfaces and added more anntotation tools
  • Structural annotation only

Version 1.0 (2011)

  • Designed to annotate BAC clones so only smaller pieces of DNA were allowed, not whole genomes
  • Separate web page interface for job creation and to browse results (custom browser)
  • Structural annotation only