ViralMSA v1.1.44

• Move reference genome dictionary back into ViralMSA script to make it easy/fast to run

ViralMSA v1.1.43

• Removed GUI (people should use the web app instead)
• Restructured how reference genome list is loaded
  • It now pulls from here: https://github.com/Niema-Lab/Reference-Genomes
  • This means internet connection is required to pull the list, but given that the list is only used to download genomes from NCBI, it's useless offline anyways
  • Offline execution still works fine (including by passing in NCBI NC_* ID)

ViralMSA v1.1.42

• Added Measles reference genome
• Renamed "Monkeypox" to "Mpox"
• Added aliases for some viruses
  • COVID-19 --> SARS-CoV-2
  • SC2 --> SARS-CoV-2
  • Monkeypox --> Mpox (to avoid breaking existing pipelines)

ViralMSA v1.1.41

• Added number of sequences in input file to log
  • This is useful for debugging
  • I also added the number of sequences in the output file as well, but only if there's a mismatch (i.e., the "WARNING" message shows)

ViralMSA v1.1.40

• Added seq-align
  • This is very slow!!! It should only be used when the other read mappers fail to align sequences

ViralMSA v1.1.39

• Added BWA (using the BWA-MEM algorithm)

ViralMSA v1.1.38

• Renamed "Chikungunya virus" to "CHIKV"

ViralMSA v1.1.37

• Added Chikungunya virus reference genome (NC_004162)

ViralMSA v1.1.36

• Moved Biopython check to only occur if the user is trying to download a remote reference genome
  • This way, if the user is using a local reference genome, we don't need to have Biopython installed

ViralMSA v1.1.35

• Fixed missing Biopython dependency in Docker image
  • Thanks, @lecorguille!
• Updated dependency versions in Docker image