viral-genomics

There are 1 repository under viral-genomics topic.

• WrightonLabCSU / DRAM

  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

  bioinformaticsgenomicsmetagenome-assembled-genomesmetagenomicsviral-genomicsviral-metagenomicsannotationmicrobiome
  Language:Python 237
• vipr

  nf-core / vipr

  Assembly and intrahost / low-frequency variant calling for viral samples

  nf-corenextflowworkflowviralviral-genomicsvariant-callingmetagenomicsgenome-assemblyviral-ngsviral-metagenomicsvirusesviruspipeline
  Language:Nextflow 14

• hzi-bifo / Quasimodo

  QuasiModo: Assessing viral genomic analysis methods on HCMV strain mixture

  viral-genomicsmetagenomicsbenchmarking
  Language:C++ 13

• agudeloromero / EVEREST

  Viral genome assemble and characterisation

  genome-analysisgenome-annotationgenome-assemblyviral-genomicsviral-metagenomicsviral-ngs
  Language:Python 10

• jonas-fuchs / virHEAT

  Visualize microbial evolution at the SNP level!

  genome-visualizationheatmappypi-packagesnpsvariant-analysisvcf-filesviral-genomics
  Language:Python 10

• ucsd-ccbb / C-VIEW

  This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.

  viral-genomicsepidemiologysequencing
  Language:Python 9

• broadinstitute / bvas

  bvas: bayesian viral allele selection

  bayesiansars-cov-2sars-cov-2-variantsviral-genomicspyropytorch
  Language:Python 8

• gFedonin / VirGenA

  A reference guided assembler of highly variable viral genomes

  bioinformaticsgenome-assemblyngsviral-genomicsviral-ngs
  Language:Java 8

• will-rowe / artic-tools

  a set of tools for viral amplicon schemes

  articamplicon-sequencingviral-genomicsnanopore
  Language:C++ 6
• uvaia

  quadram-institute-bioscience / uvaia

  Reference-based alignment and sequence database search of SARS-CoV-2 genomes.

  alignmentbioinformaticsgenomicsnearest-neighbor-searchsars-cov-2search-algorithmviral-genomics
  Language:C 4

• cvisb / cvisb_data

  Data portal and API for Center for Viral Systems Biology (CViSB) data

  biologysystems-biologysystemsbiologyviral-genomicsviral-metagenomicsviral-alleleviral-diversityviral-ngsebolaebola-outbreaklassalassa-feverhlahla-typinghla-databaseimmunologyimmunological-bioinformaticssequencingngs-data
  Language:TypeScript 3

• gallardo-seq / MrHAMER

  High accuracy single molecule Nanopore reads using the MrHAMER pipeline

  amplificationbioinformaticshivmedakananoporenanopore-sequencingpolisherporechopraconsingle-molecule-sequencingviral-evolutionviral-genomics
  Language:Python 2

• khourious / vgapONT

  Viral genome assembly pipeline for WGS using ONT

  minionviral-genomicswhole-genome-sequencingsars-cov-2chikungunyazikapipelinebioinformaticsgenomicsnanopore-sequencing
  Language:Shell 2

• sociovirology / human_influenza_LMGSeq

  Linked Multilocus Genotype by Sequencing (LMGSeq) applied to high-throughput quantification of genetic exchange among diverse human Influenza A virus strains

  influenzareassortmentviral-genomics
  Language:R 2

• hello-im-aryss / ViralGenomicsApp_Bis15L_R

  UC Davis: Data Science for Biologists - R markdown

  rappviral-genomics
  Language:HTML 1

• khourious / vigeas

  VIral GEnome ASsembly pipelines for WGS

  genomicsilluminaillumina-sequencingminionnanopore-sequencingviral-genomicswhole-genome-sequencing
  Language:Shell 1

• schultzm / havic

  Detect Hepatitis A Virus Infection Clusters

  viral-genomicstransmissioncluster-analysisphylogenomics-pipeline
  Language:Python 1

• STTLab / HIV-64148

  HIV-64148, an integration of multiple long-read genome assemblers with a pipeline for analysis of HIV-1 genomic data from Oxford Nanopore Sequencing Technology or PacBio Real-Time (SMRT) Sequencing technology.

  genomic-surveillancehaplotype-assemblyhivnanopore-analysis-pipelineviral-genomics
  Language:Python 1

• alepfu / vog-eda

  EDA of virus orthologous groups (VOGs) from VOGDB and eggNOG

  orthology-inferenceviral-genomicseda
  Language:Jupyter Notebook 0

• Alepidoptera7 / k-means-to-BLAST-

  Uses k-means prediction to ascertain genomic sequences within ambiguously attributed fasta format data. The resulting cluster sequences are used to develop NCBI BLAST requests.

  genomicsk-means-clusteringmachine-learningviral-metagenomes-analysisviral-metagenomicsbiopythonviral-genomicsarchaeal-genomicstranscriptomics
  Language:Python 0

• CanCOGeN-V / irida-plugin-viral-amplicon-consensus-variants

  Sequence Analysis Pipeline for the IRIDA Platform for Viral Genomes

  sequence-analysisviral-genomicsmicrobial-genomicsvariant-calling
  Language:Java 0

• vpeddu / CMV-NIPT

  Hunting for CMV and HHV-6 in cfDNA sequence

  cell-free-dnabioinformatics-pipelineviral-genomicsnext-generation-sequencingngs-analysis
  Language:R 0

• acharyak184 / Kamal-Acharya

  Kamal_Acharya

  photographyphotossmileviral-genomics

• akarazeev / LauzHack19

  🇨🇭🦠 Service for pathogens and threats identification in hospital environments - SOPHiA Genetics

  pathogensbiopythonncbirefseqviral-genomicsbrain-infectionslauzhacklauzhack2019voila
  Language:Jupyter Notebook

• biocyberman / viral-ngs

  Viral genomics analysis pipelines

  ngsbioinformaticsviral-genomics
  Language:Python

• caleblareau / hhv6-reactivation

  Repository for analyses of HHV-6 reactivation using genomics

  car-tngssingle-cellviral-genomics
  Language:HTML

• giffordlabcvr / NCBI-HCV-GLUE

  Extension to HCV-GLUE - contains all published HCV data from NCBI, plus analysis logic for HCV genomes.

  virus-evolutionhepatitis-cmicrobial-genomicsbioinformaticsvirus-genomesbioinformatics-databasesantiviral-resistanceviral-genomics

• mkayasth / viralGeneClock--codespaces

  Python tool for relative mutation rate of different genes across viral strains.

  gene-annotationmultiple-sequence-alignmentviral-genomicsgithub-codespacesmutation-ratesneighbor-joiningflask-application
  Language:Python

• Public-Health-Bioinformatics / irida-plugin-micall-lite

  Human RNA virus genotyping

  irida-pipelinegalaxybioinformatics-pipelineviral-genomics
  Language:Java

• tomalf2 / recombinhunt-cov

  RecombinHunt (alias for the software contained in this repository) is a Python library implementing a data-driven novel method for identifying contributing lineages and breakpoints in recombinant viral sequences.

  big-databioinformaticsdata-sciencerecombinationresearchviral-genomics
  Language:Python