IDseq
IDseq is user-friendly software platform, originally developed for metagenomics studies. Functionality has
since
been added for SC2 consensus assembly calling from paired-end Illumina data.
https://www.discoveridseq.com/
Basestack
Basestack is a platform for local deployment of standardized genomic surveillance analysis tools. It
currently
enables real-time analysis of Nanopore generated sequencing data for SARS-CoV-2.
https://github.com/jhuapl-bio/Basestack
No code Phylogenetic analysis
An open source, free, no-code genomic epidemiology analysis platform for public health
https://czgenepi.org/