Note: this document is copied from the repository changelog.

Release notes

v1.1.0-rc1:

  • Support for read groups:
    • Support ‘pool’ read groups taken from BED file, e.g.:
      • nCoV2019_1
      • nCoV2019_2
    • These can be helpfully viewed in the Tablet viewer.
    • Do variant calling separately on each group, permits detection of incongruent mutations e.g. from contamination
  • Update to nanopolish 0.12.5 fo more informative VCF output
  • Change nanopore filtering to support new VCF output (e.g. strand-bias)
  • Support indels with bcftools consensus
  • Longshot added to Medaka to permit filter VCF on depth
  • New workflow model - all commands run "one per sample", script nanopolish index
  • Add 'artic gupplyplex' for support for demultiplexed Guppy output to replace 'artic gather'
  • Fix for align_trim to remove erroneous CIGAR strains that can cause medaka to fail
  • Support for amplicons v3 format file (Will Rowe)
  • Test suite (Will Rowe)
  • Documentation (Will Rowe)
  • Remove old deprecated code (Will Rowe)

v0.13:

  • ARTIC fork

v0.12:

  • Update to nanopolish v0.8.4 for Albacore 2.0+ support:
    • run nanopolish -d /path/to/fast5 input.fasta before zibra.py minion

v0.11-dev:

  • Add stringent pipeline

v0.11 (25th July 2017):

  • Revert back to Ryan Wick's porechop repo as --untrimmed now implemented
  • New script: align_trim_fasta.py and reconstitute.py as basis for more principled demultiplexing (align first, then trim to known amplicon end points +/- 40 bases) to help prevent chimeric reads resulting in incorrect barcode identification

v0.10 (15th July 2017):

  • Better handling of confident deletions (previously ignored, now N-masked)
  • Update to nanopolish HEAD
  • Fixes to support latest nanopolish VCF format changes
  • Ability to choose higher values of max-haplotypes to support more divergent references

v0.9:

  • New command line interface zibra.py to ease extraction and demultiplexing with Albacore and multiple groups

v0.8:

  • Track latest Porechop with better adaptor trimming

v0.7:

  • Add Illumina wrapper scripts

v0.6:

  • Update poretools

v0.5:

  • Update nanopolish to latest HEAD - to fix Albacore 1.1 support (7de633d01cc35a58e5537af5dd1024ae0040d15c)
  • Add Lassa virus scheme

v0.4:

  • Update nanopolish to latest HEAD - aaaf90beb4efe37243c651e62fcfd11374fe2176 for Albacore 1 support
  • Initial support for Yellow Fever (500 and 1000 bp schemes)
    • Move to poretools for extraction with named basecaller

v0.3:

  • add Porechop

v0.2:

  • update nanopolish to 0.6 - adds default support for various nanopore models
  • update samtools to 1.4