Alternatives and similar repositories for mpox:

Users that are interested in mpox are comparing it to the libraries listed below

• W-L / ProblematicSites_SARS-CoV2
  ☆49Updated 3 years ago
• cov-lineages / pangolin-data
  Repository for storing latest model, protobuf, designation hash and alias files for pangolin assignments
  ☆30Updated 3 weeks ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated 3 weeks ago
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆48Updated last year
• epi2me-labs / wf-artic
  ARTIC SARS-CoV-2 workflow and reporting
  ☆50Updated 4 months ago
• artic-network / primer-schemes
  Primer schemes for real-time genome epidemiology
  ☆27Updated last year
• pathoplexus / pathoplexus
  An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
  ☆33Updated last week
• nextstrain / nextclade_data
  Datasets for https://github.com/nextstrain/nextclade
  ☆33Updated last week
• andersen-lab / avian-influenza
  Consensus sequences for U.S. H5N1 clade 2.3.4.4b
  ☆31Updated this week
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆75Updated 3 weeks ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 2 years ago
• jhuapl-bio / taxtriage
  TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomi…
  ☆34Updated this week
• flu-crew / parnas
  Phylogenetic maximum representation sampling: choosing most representative strains or taxa
  ☆37Updated 2 weeks ago
• theiagen / public_health_viral_genomics
  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, es…
  ☆41Updated 8 months ago
• ncbi / rapt
  This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
  ☆57Updated 3 weeks ago
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆27Updated this week
• wslh-bio / spriggan
  Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
  ☆16Updated last week
• maximilianh / multiSub
  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input…
  ☆35Updated 2 years ago
• INSaFLU / INSaFLU
  INSaFLU-TELEVIR: an free web-based (but also locally installable) bioinformatics suite for virus metagenomic detection and routine genomi…
  ☆34Updated 2 weeks ago
• USDA-VS / GenoFLU
  Influenza data pipeline to automate genotyping assignment
  ☆31Updated 2 months ago
• CDCgov / seqsender
  Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
  ☆36Updated last week
• CDCgov / phoenix
  🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
  ☆72Updated this week
• cov-lineages / scorpio
  serious constellations of reoccurring phylogenetically-independent origin
  ☆39Updated last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆55Updated 7 months ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆62Updated last year
• sdellicour / seraphim
  R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al.…
  ☆33Updated 2 weeks ago
• virus-evolution / gofasta
  ☆35Updated 2 weeks ago
• theosanderson / chronumental
  Estimating time trees from very large phylogenies
  ☆26Updated 9 months ago
• flu-crew / TreeSort
  Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
  ☆13Updated 2 weeks ago
• bacpop / ska.rust
  Split k-mer analysis – version 2
  ☆82Updated 2 months ago