Note: this document is copied from the repository changelog.

Release notes


  • 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)


  • ARTIC fork


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


  • Add stringent pipeline

v0.11 (25th July 2017):

  • Revert back to Ryan Wick's porechop repo as --untrimmed now implemented
  • New script: and 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


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


  • Track latest Porechop with better adaptor trimming


  • Add Illumina wrapper scripts


  • Update poretools


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


  • 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


  • add Porechop


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