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RAMPART. Read Assignment, Mapping, and Phylogenetic Analysis in Real Time. RAMPART runs concurrently with MinKNOW and shows you demuxing / mapping results in real time.
RAMPART run concurrently with MinION sequencing of such pathogens. It provides a real-time overview of genome coverage and reference matching for each barcode. RAMPART was originally designed to work with amplicon-based primer schemes (e.g. for ebola ), but this isn't a requirement.
Step 1: Create a new conda environment or install nodejs into your current conda environment. Create a new conda environment and activate it via: conda create -n artic-rampart -y nodejs=12 # any version >10 should be fine. conda activate artic-rampart.
6 de fev. de 2020 · Read Assignment, Mapping, and Phylogenetic Analysis in Real Time - artic-network/rampart
The “protocol” is what defines how RAMPART will behave and look. It’s the primary place where the reference genome(s), primers, analysis pipelines etc are defined. For this reason a protocol is typically virus-specific, with the run-specific information overlaid.
1 de abr. de 2020 · A new version of RAMPART, our software for analyzing nanopore data in real-time, is now available. This brings a number of major changes which should help with SARS-CoV-2 analyses. There are no changes to how RAMPART is run.
