Releases: Aveglia/vAMPirus
vAMPirus v2.0.5 - Polymerase II
vAMPirus v2.0.4 - Polymerase II
v2.0.4 - Test for yaml files
vAMPirus v2.0.3 - Polymerase II
Fixed errors caused by skip options and typos in code in v2.0.2.
vAMPirus v2.0.2 - Polymerase II
fixed phylogeny-based clustering processes
vAMPirus v2.0.1 - Polymerase II
Added phylogeny-based sequence clustering with the program TreeCluster and made more parameters customizable for read processing.
vAMPirus v2.0.0 - Polymerase I
New in vAMPirus v2.0.0
1- (EXPERIMENTAL) Added Minimum Entropy Decomposition analysis using the oligotyping program produced by the Meren Lab. This allows for sequence clustering based on sequence positions of interest (biologically meaningful) or top positions with the highest Shannon's Entropy (read more here: https://merenlab.org/software/oligotyping/ ; and below).
2- Added more useful taxonomic classification of sequences leveraging the RVDB annotation database and/or NCBI taxonomy files (see manual for more info).
3- Replaced the used of MAFFT with muscle v5 (Edgar 2021) for more accurate virus gene alignments (see https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full).
4- Added multiple primer pair removal to deal with multiplexed amplicon libraries.
5- ASV filtering - you can now provide a "filter" and "keep" database to remove certain sequences from the analysis
6- Reduced redundancy of processes and the volume of generated result files per full run (Example - read processing only done once if running DataCheck then Analyze).
7- Color nodes on phylogenetic trees based on Taxonomy or Minimum Entropy Decomposition results
8- PCoA plots added to Analyze report if NMDS does not converge.
vAMPirus v1.0.1 - Capsomere I
Initial release of vAMPirus, an automated and comprehensive virus amplicons sequencing analysis program integrated with the workflow manager Nextflow.