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CHANGELOG
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CHANGELOG
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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