Version 0.7.0

This is the first tagged release in a while, and importantly, the first release since releasing the preprint. It has a lot of breaking changes when compared to v0.6 and also to the pandora_paper_tag1 tag.

Added

• discover subcommand for de novo variant discovery [#234]
• many more tests

Changed

• FASTA/Q files are now parsed with klib [#223]
• command-line interface is now overhauled with many breaking changes
  [#224]
• global genotyping has been made default [#220]
• Various improvements to VCF-related functions

Fixed

• k-mer coverage underflow bug in LocalPRG [#183]

0.6

Now with a dockerfile.

Pre-release

• Index, map and compare are now more stable
• Includes initial implementation of de novo discovery
• With multi-threading, indexing now takes ~30 minutes on 16 threads to index an E. coli PanRG with 35,000 local graphs representing genes and intergenic regions
• Compare not yet optimized : with 124GB RAM on a single core, can expect to be able to compare 16 Nanopore samples with 30X coverage each, or 16 Illumina samples with 20X coverage (just)

First pre-release

Allows consensus sequence inference and genotyping for nanopore and illumina data for a single sample read dataset