v1.4.0

• Smaller container sizes
• Fix to work on larger genomes (eg mpox) by using mafft for global alignment instead of current nucmer-based method. New default is to use mafft if reference genome is longer than 30kbp, so covid is not affected
• Add command line option --force_mafft to use mafft for global alignment regardless of reference genome size

v1.3.1

Bug fix: forcing the amplicon scheme was not happening (the log said it was, but best scoring was actually still being used)

v1.3.0

• Add support for primer schemes in PrimalScheme formatted BED files
• Fix bug where when downloading reads and running, and reads failed to download, tried to delete some files that didn't exist

v1.2.2

Bug fix: version flag of previous version 1.2.0 was not updated. This release is to fix that, so it now reports 1.2.2.

v1.2.1

Bug fix where if there the pipeline would stop if there was only one amplicon scheme, because the second best score didn't exist (issue #111)

Known issue with this release: the --version flag was not updated, and still reports 1.2.0.

v1.2.0

• Added new command line task dl_and_run, to download and run a batch of reads
• changed name of options --ena_run -> --run_accession; --keep_ena_reads -> --keep_downloaded_reads
• fixed bug where downloaded reads had to be paired. Now unpaired works
• fixed bug where --tech option had to be specified when downloading reads

v1.1.0

Allow Illumina reads to be unpaired

v1.0.0

• main script called viridian (viridian_workflow also kept for backwards compatibility, they are actually the same scripts)
• improved scheme detection, using mapped fragment ends to make a normalised score, and remove unseen primers
• add schemes artic5 and varskip
• add ion torrent support
• command line option to simulate fragments from reads and get the scheme scores
• output MSAs for tree building
• option to get reads from bam or download from ENA
• optionally run ReadItAndKeep
• plots of scheme score results and depth across genome
• qc TSV and masking includes handling indels and ambiguous IUPAC codes
• various bug fixes and other small improvements

v0.3.7

Add auto built Docker image to github containers

v0.3.6

Internal release, better handling of fragmented consensus sequences