Alternatives and similar repositories for GISAIDR:

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

• sherrillmix / taxonomizr
  Parse NCBI taxonomy and accessions to find taxonomic assignments
  ☆70Updated 3 weeks ago
• drostlab / orthologr
  Genome wide orthology inference and dNdS estimation
  ☆88Updated last year
• simon-ho / SydneyPhyloWorkshop
  Sydney Phylogenetics Workshop
  ☆63Updated last week
• Sydney-Informatics-Hub / Shotgun-Metagenomics-Analysis
  Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more
  ☆27Updated last year
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆96Updated 4 months ago
• victoriapascal / gutsmash
  gutSMASH
  ☆54Updated 3 weeks ago
• SvetlanaUP / Microbiome-etc-Podcasts
  This repo collects the list of podcasts related to microbiome science: science, microbiology and bioinformatics.
  ☆23Updated last month
• bjtully / BioData
  All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")
  ☆70Updated last year
• smdabdoub / kraken-biom
  Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…
  ☆50Updated 2 years ago
• hildebra / lotus2
  Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.
  ☆53Updated last week
• AstrobioMike / bit
  Bioinformatics Tools
  ☆81Updated this week
• Russel88 / DAtest
  Compare different differential abundance and expression methods
  ☆50Updated 2 years ago
• Gibbons-Lab / isb_course_2023
  Materials and presentation for the 2023 ISB Microbiome course.
  ☆24Updated 3 months ago
• statdivlab / radEmu
  ☆51Updated this week
• moshi4 / COGclassifier
  A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
  ☆59Updated 4 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
  ☆53Updated 4 months ago
• transcript / samsa2
  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…
  ☆57Updated 9 months ago
• christophertbrown / iRep
  scripts for estimating bacteria replication rates based on population genome copy number variation
  ☆70Updated 5 years ago
• jodyphelan / genomics_course
  ☆11Updated last year
• karkman / MetagenomeCourse2019
  Course material for the metagenomics course
  ☆43Updated 2 years ago
• knights-lab / SHOGUN
  SHallow shOtGUN profiler
  ☆54Updated 2 years ago
• UPHL-BioNGS / Cecret
  Reference-based consensus creation
  ☆51Updated this week
• EBI-Metagenomics / mettannotator
  ☆57Updated 3 weeks ago
• arumugamlab / msamtools
  Metagenomics-related extended functionalities to samtools
  ☆19Updated last year
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆70Updated 2 years ago
• bhattlab / kraken2_classification
  Snakemake workflow for metagenomic classification with Kraken2
  ☆65Updated last year
• Lagkouvardos / Rhea
  A set of R scripts for the analysis of microbial profiles
  ☆41Updated 7 months ago
• treangenlab / emu
  ☆41Updated last month
• nvelden / geneviewer
  An R package designed for drawing gene arrow maps
  ☆36Updated this week
• gtonkinhill / fastbaps
  A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
  ☆59Updated 2 years ago