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CHANGELOG.md

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v1.1

Features

  • Added support for ONT sequencing platform
  • Added option to skip comparative analyses

Enhancements

  • Updated CARD db
  • Updated VF db
  • Applied many bugfixes and minor improvements to report pages

v1.0.4

##Enhancements

  • Updated NCBI tbl2asn
  • Fixed VF reports bug introduced by CARD/ResFinder replacement

v1.0.3

Enhancements

  • Added option to skip comparative analyses
  • Applied many bugfixes and minor improvements to report pages
  • Replaced ResFinder by CARD as annotation database
  • Harmonized variable names in cloud property file
  • Fixed NPE in ANI calculation

v1.0.2

Enhancements

  • Applied many bugfixes and minor improvements

v1.0.1

Enhancements

  • Applied many bugfixes and minor improvements

v1.0

Features

  • Added support for PacBio Sequel protocol
  • Added a virulence factor (VF) detection analyses based on VFDB

Enhancements

  • Fixed PacBio analysis workflow
  • Fixed internal step selection
  • Reviewed QC contamination plots
  • Added comprehensive help sections to report pages
  • Applied many bugfixes and minor improvements to report pages
  • Replaced ResFinder by CARD as annotation database

v0.9

Features

  • Added a 16S rRNA based taxonomic classification
  • Added a core/pan genome analysis
  • Replaced CONTIGuator by MeDuSa (single -> multi reference based scaffolding)

Enhancements

  • Updated annotation databases (Refseq Feb 17)
  • Updated annotation databases (RFAM 12.2)
  • Updated ABR database (CARD 1.1.8)
  • Adjusted SGE CPU/RAM resource requests
  • Applied many bugfixes and enhancements to HTML report pages

v0.8

Features

  • Added an antimicrobial resistance detection analysis based on CARD db
  • Added a MLST analysis
  • Added support for draft reference genomes
  • Added ANI computation for references
  • Added a length and coverage based contig filter after assembly

Enhancements

  • Reorganized and improve all report pages
  • Decoupled ASA³P from BCF ressources
  • Added ResFinder and VFDB as annotation reference databases
  • Provided Prokka with gram +/- information
  • Updated annotation databases (RFAM 12.1)
  • Provided unique locus tags to contigs during annotation

v0.7

  • Reimplemented cluster scripts
  • Annotate SNPs with SnpEff
  • Added circular genome plot to annotation report

v0.6

  • Handle failed/skipped steps
  • Added interactive JS visualizations
  • Several bugfixes and minor improvements

v0.5

  • Added an phylogeny analyses
  • Added a reporting stage creating HTML reports