Sequence analysis tools

COVID-19 analysis on usegalaxy https://covid19.galaxyproject.org/

https://observablehq.com/@spond/natural-selection-analysis-of-sars-cov-2-covid-19 (Live code for natual selection analysis)

http://covid19.datamonkey.org (Natural Selection Analysis)

A cloud-based computational platform that provides pre-built workflows for a variety of analyses, including genomics, evolution, cheminformatics, direct RNAseq, and proteomics; powered by Galaxy
For Natural Selection Analysis, GISAID data are analyzed daily by the Datamonkey and HyPhy team; published in: bioRxiv

SARS-CoV-2: ViPR (Virus Pathogen Resource) https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov

An integrated repository of data and analysis tools for multiple virus families
Includes search tools for various databases (sequence & strains, immune epitopes, antivirus drugs, etc.) and various analysis tools (BLAST, MSA, genome annotator, SNP analysis, phylogeny, etc.)
Workbench can be public or private

The Broad Terra cloud workspace for best practices for analyzing COVID-19 genomics data https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19/notebooks

Provides a cloud-based computational platform with pre-built workflows; similar to Galaxy
Raw sequencing data (.fastq and .BAM) from NCBI SRA available
Workflows include genome assembly, quality control, metagenomic classification, phylogenetic analysis, and more
Supports only Chrome; Google account required
Interface is somewhat not intuitive

Pangolin SARS-CoV-2 Lineage Assigner (Phylogentic Assignment of Named Global Outbreak LINeages) https://pangolin.cog-uk.io

https://github.com/cov-lineages/pangolin (Software)

https://github.com/hCoV-2019/lineages/ (Lineage summary and companion data)

Guide tree and alignment based SARS-CoV-2 lineage prediction tool
Published in: https://doi.org/10.1038/s41564-020-0770-5

Coronavirus Typing Tool https://www.genomedetective.com/app/typingtool/cov/

Uses Genome Detective Virus Tool for phylogeny-based coronavirus classification
Reference genomes include SARS-CoV-2, SARS-CoV, and SARS-related CoV (only representatives are included)
Genome Detective Virus Tool can be used to asseemble NGS short reads (FASTQ)

CoVDB http://covdb.popgenetics.net/v3/

A collection of published coronavirus data from 32 organisms documented since 1941
Tools provided include genome browser, various searches (BLAST, subcellular location, and functions), genomic and protein sequence comparison between strains, population and phylogenetic analyses, and gene clusters
Browser-specific rendering; interface is rather slow and somewhat not intuitive