Alternatives and similar repositories for MicrobeTrace

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

• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆55Updated 2 years ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated last year
• roblanf / sarscov2phylo
  Global phylogenies of SARS-CoV-2 sequences
  ☆86Updated last year
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated last month
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year
• CDCgov / tostadas
  🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
  ☆28Updated this week
• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆75Updated 3 months ago
• phylogeography / SpreaD3
  Spatial Phylogenetic Reconstruction of Evolutionary Dynamics 3
  ☆16Updated 2 years ago
• viralemergence / virion
  An open database of vertebrate-virus interactions
  ☆41Updated last week
• aomlomics / tourmaline
  Amplicon sequence processing workflow using QIIME 2 and Snakemake
  ☆47Updated 3 weeks ago
• sdellicour / seraphim
  R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics)
  ☆34Updated last week
• W-L / ProblematicSites_SARS-CoV2
  ☆49Updated 3 years ago
• pha4ge / SARS-CoV-2-Contextual-Data-Specification
  Collection template and associated materials for SARS-CoV-2 metadata
  ☆35Updated last year
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated this week
• nextgenusfs / amptk
  AMPtk: Amplicon ToolKit for NGS data (formally UFITS)
  ☆38Updated last year
• CDCgov / phoenix
  🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
  ☆76Updated this week
• CDCgov / MIRA
  MIRA: Portable, Interactive Application for High-Quality Influenza, SARS-CoV-2 and RSV Genome Assembly, Annotation, and Curation
  ☆18Updated last month
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated last year
• pha4ge / pipeline-resources
  Bioinformatics Pipeline and Visualization resources
  ☆56Updated 10 months ago
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆49Updated 9 months ago
• biocore / redbiom
  Sample search by metadata and features
  ☆47Updated last year
• 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…
  ☆36Updated 3 years ago
• snayfach / IGGsearch
  Metagenomic species profiling with enhanced coverage of the human gut microbiome
  ☆25Updated last year
• theosanderson / taxonium
  A tool for exploring large trees in the browser
  ☆111Updated 2 weeks ago
• borenstein-lab / burrito
  A visualization tool for exploratory data analysis of metagenomic data
  ☆37Updated 3 years 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.
  ☆58Updated 3 months ago
• GenomicsAotearoa / metagenomics_summer_school
  Course materials for the Genomics Aotearoa Metagenomics Summer School, to be hosted at the University of Auckland in Septermber
  ☆61Updated 10 months ago
• snayfach / IGGdb
  Database of genomes integrated from the gut microbiome and other environments
  ☆45Updated 2 years ago
• KasperSkytte / ampvis2
  Tools for visualising microbial community amplicon data
  ☆67Updated 3 months ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 3 years ago