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Original repo by Aine Niamh O'Toole - https://github.com/aineniamh/realtime-noro.git
Previous upload contained changes I made remotely. These files are the true starting point - https://github.com/aineniamh/realtime-noro.git
Added goals of Spring 2020 project to head
Original only accounted for 4 multiplexed samples. Our runs tend to be 24 multiplexed samples per run
Updated genotyping numbers of original fasta file. Added more genomes to represent each of the 77 noroviruses.
Used aligned version of GI.1 - contains N's to accommodate longer noro sequences during mapping
Dropped minimum reads to allow for consensus to be obtained in low coverage regions of the genome
Changed min ID and VP1 cutoff values to match other updated files in package
RAMPART had since been updated by another team and required different packages to run properly. Environment recommendations are taken from the most recent installment of RAMPART projects - SARS-CoV-2 (ncov2019) - https://github.com/artic-network/artic-ncov2019
Every possible amplicon combination was determined for each of the 77 norovirus genotypes
RAMPART instructions updated - still need to establish correct consensus building instructions (the original instructions above do not work)
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To summarize our chat.... Given the complex dependencies of the project, most of your effort will go into simply creating the package and adding some tests.
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superseded by #32 |
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