New Features and Updates

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

Version 6.0 (September 2018)

  • GenSAS provided BLAST databases updated to current versions (7/7/2023)
  • GenSAS transitioned to use SLURM scheduler instead of SGE, tools were updated to current versions (March 2022)
  • Tools updated to current verison: RepeatMasker, RepeatModeler, GeneMarkES, BLAST+, pBLAT, DIAMOND, HISAT2, PASA, SignalP, TargetP, BUSCO, InterProScan (Summer 2021)
  • 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