v1.0.2

Minor fixes and models release.

• R9.4.1 variant calling models for Guppy 3.6.0 and updated benchmarks.
• Made r941_min_high_g360 the default consensus model.
• VCF GQ is now an integer in line with VCF spec.
• Fixed issue requiring a previous model for training.
• Fixed issue causing -p option of medaka_variant to crash.
• Fixed issue preventing installation in a virtualenv with python <3.6.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v1.0.1

Minor fixes release, resolving issues introduced in v1.0.0.

• Fix default model for SNP calling.
• Fix issue causing medaka_consensus to crash.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v1.0.0

Models, features and fixes release

• Consensus models for Guppy 3.6.0.
• Add functionality for auto-download of older models.
• Fix to methylation aggregation.
• VCF annotation tool.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.12.1

Minor release harmonising versions of htslib/samtools dependencies.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.12.0

Models, features and fixes release

• Variant calling models for R10.3 and R9.4.1 and updated benchmarks.
• Consensus models for Guppy 3.5.1.
• Add read group (RG) tag filtering.
• Add option to create consensus sequence via intermediate .vcf file.
• Update to methylation calling documentation.
• Addition of all-context modified-base aggregation.
• Minor speed improvement.
• Fix bug where force overwrite of output was always enabled.
• Fix bug where variant calling of a region crashed if the region began with a deletion.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.11.5

R10.3 model and small fixes

• Add model for R10.3 on MinION.
• Fix index/compression issue with RLE workflow
• Write an empty vcf when no variants are found in medaka_variant.
• Fix a rare memory error during feature generation caused by very long indels.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.11.4

Bugfix

• Fix invalid specification of variant calling model.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.11.3

Model release

• Models for guppy 3.4.4.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.11.2

Minor fix release

• Fix a memory error in pileup calculation.
• Update variant calling models (improved indel performance) and benchmarks.

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.

v0.11.1

Minor Release

• Preliminary hard-RLE model for R9.4.1
• --regions argument can now be a .bed file.
• Detect NaNs during training and halt early.
• Workaround pysam interface changes (for conda package).
• Support soft-RLE network training.

This release includes an experimental consensus mode using run-length encoded alignments. Use of this algorithm can be specified using the new "rle" model:

medaka_consensus -m r941_min_high_g340_rle -i basecalls.fasta -d draft.fa

Please do not attempt to use the "Source code" assets attached below for running medaka, they do not include medaka's model files.