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Sequence analysis tools

TitleURLFeatures
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)
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