Last release for version 1.xx series

I am now focussed on version 2.0. This is the last release for the 1.x series. I'm not sure what's changed since 1.28 as I co-developing v2 and it is confusing. Personally, I would wait for v2. Sorry!

Where do I start!

• Lots of bug fixes!
• Way more pretty CSS + Datatables layout
• Way faster roary2svg.pl
• Way faster pairwise SNPS using snp-dists
• Using EMBOSS for FASTA conversion
• Embed pan-genome as SVG instead of PNG
• Better error handling
• New --gcode option for weird samples
• Now default is auto MLST detection
• New Virulome table
• Example reports online
• Better documentation
• Removed legacy cruft

Don't say I didn't warn you

Forgot to incoude the trimmomatic adapters.fa file in 1.00. D'oh.

Stability is all relative

The first "official" release:

• vertical resistome reports
• more compact trees
• use trimmomatic instead of skewer
• more Makefile targets inc. "make help"
• pan-genome tree and picture
• better megahit assemblies

More good stuff

Fixed bugs found when trying to deploy on the Genomics Virtual Lab VM.

I just feel like it edition.

Lots of new stuff but still not perfect

• better Makefile
• some auto MLST detection
• pan-genomes!
• lovely colourful QC ticks

Halloween Edition

Lots of changes

• pan genome output
• improved makefile
• insert sizes
  And more!

Lots of fixes

v0.6

Issue #27 resolved - ensure Kraken stuff is set up

Usable brew

v0.4

Make suitable for Brew packaging