vAMPirus v2.0.0 (Polymerase I) - An automated, comprehensive virus amplicon sequencing analysis program
| Main Authors: | Alex Veglia, Ramon Rivera, Carsten Grupstra, Lauren Howe-Kerr, Adrienne Correa |
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| Format: | info software Journal |
| Terbitan: |
, 2021
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/5563088 |
Daftar Isi:
- 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.