| Variant Effect Predictor
|| In response to COVID-19, Ensembl VEP extended its support for SARS-CoV-2. The tools annotate variants and find the effect of variants. It analyzes variants against the SARS-CoV-2 gene set from Ensembl.
|| Variant annotation and interpretation
W. McLaren, L. Gil, S.E. Hunt, H.S. Riat, G.R. Ritchie, A. Thormann, et al.
| The Ensembl Variant Effect Predictor
| Infectious Pathogen Detector (IPD)
|| Infectious Pathogen Detector (IPD) is an automated pathogen analysis pipeline developed by ACTREC, Tata Memorial Centre. IPD performs mutation analysis with respect to the Wuhan reference sequence and, based on the mutations assign sample to the phylogenetic clade. It also performs systematic quantification of pathogen genomes.
|| Quantification, mutation analysis and phylogeny
|| Sanket Desai, Sonal Rashmi, Aishwarya Rane, Bhasker Dharavath, Aniket Sawant, Amit Dutt
|| An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome
|| CoVPipe is a pipeline developed for reliable and fast analysis of SARS-CoV-2 data. It has a fully automated workflow for the reference-based reconstruction of SARS-CoV-2 genomes based on next-generation amplicon sequencing data and is freely avialable on github. Thus, the workflow generates consensus sequences from NGS reads based on a reference sequence.
|| Assembly, Variant Analysis and taxonomy assignment
|| poreCov enables rapid and reliable analysis of hundreds of SARS-CoV-2 raw sequence data sets or genomes. This workflow pipeline can process nanopore's ARTIC protocol data and is freely available on github.
|| Assembly, mutation analysis and phylogeny
|| Christian Brandt, Sebastian Krautwurst, View ORCID ProfileRiccardo Spott, Mara Lohde, Mateusz Jundzill, View ORCID ProfileMike Marquet, View ORCID ProfileMartin Hölzer
|| poreCov - an easy to use, fast, and robust workflow for SARS-CoV-2 genome reconstruction via nanopore sequencing
|| VADR is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.
|| Alejandro A. Schaffer, Eneida L. Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi & Eric P. Nawrocki
|| Title of the paper: VADR: validation and annotation of virus sequence submissions to GenBank
|| V-pipe is a bioinformatics pipeline that integrates various computational tools for the analysis of viral high-throughput sequencing data. It supports the reproducible analysis of genomic diversity in intra-host virus populations, which is often involved in viral pathogenesis and virulence.
|| Alignment, Sequence variations
|| Susana Posada-Cespedes, David Seifert, Ivan Topolsky, Kim Philipp Jablonski, Karin J Metzner, Niko Beerenwinkel
|| V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data
|| Haploflow is a de Bruijn graph-based assembler for de novo genome assembly of viral strain from mixed sequence data using a novel flow algorithm. Haploflow releases 0.1 is freely available under the GPLv3 license.
|| A. Fritz, A. Bremges, Z.-L. Deng,T.R. Lesker, J. Götting, T. Ganzenmuller, A. Sczyrba, A. Dilthey, F. Klawonn, A.C. McHardy
|| Haploflow: Strain-resolved de novo assembly of viral genomes
|| VIRify is a pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The Pipeline uses nextflow and CWL execution and easy configuration using Docker container.
|| Detection, Annotation, Phylogeny
|| VIRULIGN is a tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins. VIRULIGN is freely available at GitHub as an open-source software project.
|| Alignment, Annotation
|| Pieter J K Libin, Koen Deforche, Ana B Abecasis, Kristof Theys
|| VIRULIGN: fast codon-correct alignment and annotation of viral genomes
|| CoVsurver is a Mutation Analysis tool of COVID-19. The server automatically determines the type of input (either protein or nucleotide) and compares the given input sequence to the closest reference sequence among current strains to find the present mutation. The analysis takes ~10 seconds per sequence in automatic mode. CoVsurver displays the list of amino acid changes, % amino acid identity, best reference hit, and clade information for the query sequence. The mutation summary table report is downloadable.
|| Mutation and Variation detection, Structural visuvalization, Molecular interaction, Phylogeny
|| A*STAR Bioinformatics Institute (BII), Singapore
|| An interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses. InterARTIC is a free, open-source web application implemented in Python.
|| NGS analysis
|| James M. Ferguson, Hasindu Gamaarachchi, Thanh Nguyen, Alyne Gollon, Stephanie Tong, Chiara Aquilina-Reid, Rachel Bowen-James, Ira W. Deveson
|| InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses
| COVID-19 Viral Genome Analysis Pipeline
|| This analysis pipeline tracks SARS-CoV-2 mutations in the COVID-19 pandemic and is based on regular updates from the GISAID SARS-CoV-2 sequence database. The web app provides visualizations and summary data that allow regional tracking of SARS-CoV-2 mutations over time.
|| Sequence analysis, alignment, Tracking mutations, Sequence Locator, Modeling variants
|| Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI*, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, and Montefiori DC
|| Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus.
|| MicroGMT is a python-based package, which identifies, annotate, and characterizes small indels and point mutations in the microbial genomes. Thus, MicroGMT tracks genomic mutations for the SARS-CoV-2 virus.
|| Sequence comparison and mutation annotation
|| Yue Xing, Xiao Li, Xiang Gao, Qunfeng Dong
|| MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences
|| Covidoutcome is a free web resource that takes a viral sequence as the input and gives out a list of mutations and links mutation signature to patients disease severity.
|| Mutations, Disease Severity
|| Adam Nagy, Balazs Ligeti, Janos Szebeni, Sandor Pongor, and Balazs Gyorffy
|| COVIDOUTCOME-estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome
| Virus Pathogen Resource (ViPR)
|| Virus Pathogen Resource (ViPR) is a suite of bioinformatics analysis and visualization tools. It integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank) and allows to search genome, genes, and protein sequences. The tool suits identify similar sequences, Align and visualize aligned sequences, analyze SNPs, perform metadata sequence analysis, genome assembly, and annotations, generate a phylogenetic tree, design PCR primer.
|| Align, visualize, genome assembly, and annotations, design PCR primer, metadata sequence analysis, Multiple sequence alignment, BLAST
|| Pickett et al.
|| ViPR: an open bioinformatics database and analysis resource for virology research