Alternatives and similar repositories for sarscov2phylo

Users that are interested in sarscov2phylo are comparing it to the libraries listed below

• Wytamma / GISAIDR
  Programmatically interact with the GISAID database.
  ☆78Updated 2 months ago
• artic-network / civet
  Cluster Investigation & Virus Epidemiology Tool
  ☆50Updated 4 months ago
• xavierdidelot / TransPhylo
  Reconstruction of transmission trees using genomic data
  ☆63Updated 2 years ago
• lskatz / awesome-bioinformatics-education
  resources for bioinformatics education
  ☆88Updated 5 months ago
• jts / ncov-tools
  Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  ☆49Updated last year
• BDI-pathogens / phyloscanner
  Phylogenetics between and within hosts at once, all along the genome.
  ☆50Updated last year
• bhattlab / bhattlab_workflows
  Computational workflows for metagenomics tasks, by the Bhatt lab
  ☆47Updated 2 years ago
• arpcard / amr_curation
  A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curat…
  ☆63Updated last month
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆104Updated 8 months ago
• niemasd / TreeCluster
  Efficient phylogenetic clustering of viral sequences
  ☆89Updated this week
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆53Updated 3 years ago
• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆77Updated 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
  ☆66Updated last year
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆91Updated last month
• merenlab / illumina-utils
  A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
  ☆92Updated last year
• CDCgov / datasets-sars-cov-2
  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
  ☆57Updated 2 years ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆58Updated last year
• Mykrobe-tools / mykrobe
  Antibiotic resistance prediction in minutes
  ☆112Updated 11 months ago
• COG-UK / grapevine
  Process consensus file for COG-UK data
  ☆14Updated 4 years ago
• microgenomics / tutorials
  In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given…
  ☆84Updated 7 years ago
• sdellicour / seraphim
  R package for studying phylogenetically-informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al., in prep.)
  ☆36Updated 2 weeks ago
• mgalardini / pyseer
  SEER, reimplemented in python 🐍🔮
  ☆125Updated 5 months ago
• nmquijada / tormes
  Making whole bacterial genome sequencing data analysis easy
  ☆113Updated 6 months ago
• sanger-pathogens / iva
  de novo virus assembler of Illumina paired reads
  ☆57Updated 4 years ago
• PoonLab / covizu
  Rapid analysis and visualization of coronavirus genome variation
  ☆48Updated last month
• lczech / gappa
  A toolkit for analyzing and visualizing phylogenetic placement data
  ☆62Updated 2 weeks ago
• neherlab / pan-genome-visualization
  Visualization of the pan-genome output by panX
  ☆65Updated 4 months ago
• pierrebarbera / epa-ng
  Massively parallel phylogenetic placement of genetic sequences
  ☆84Updated 3 years ago
• yatisht / usher
  Ultrafast Sample Placement on Existing Trees
  ☆134Updated last month
• ukhsa-collaboration / variant_definitions
  ☆74Updated last year