Alternatives and similar repositories for dada2:

Users that are interested in dada2 are comparing it to the libraries listed below

• picrust / picrust2
  Code, unit tests, and tutorials for running PICRUSt2
  ☆332Updated this week
• joey711 / phyloseq
  phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; an…
  ☆593Updated 8 months ago
• microbiome / microbiome
  microbiome R package
  ☆289Updated last month
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆390Updated last week
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆635Updated last month
• LangilleLab / microbiome_helper
  A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
  ☆440Updated 3 weeks ago
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆367Updated last year
• wilkox / gggenes
  ➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
  ☆521Updated 10 months ago
• jbisanz / qiime2R
  Import qiime2 artifacts to R
  ☆161Updated last month
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆409Updated last year
• taowenmicro / EasyMicrobiomeR
  Using R language in microbiome analysis
  ☆292Updated last year
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆354Updated 4 months ago
• biobakery / biobakery
  bioBakery tools for meta'omic profiling
  ☆265Updated 2 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆585Updated 8 months ago
• zdk123 / SpiecEasi
  Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
  ☆202Updated last year
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆301Updated last year
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆366Updated 2 months ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆467Updated last month
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆304Updated last year
• mothur / mothur
  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Imm…
  ☆270Updated 2 months ago
• jiabowang / GAPIT
  Genome Association Predict Integrate Tools
  ☆186Updated 2 weeks ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆329Updated 2 years ago
• ChiLiubio / microeco
  An R package for data analysis in microbial community ecology
  ☆216Updated last week
• YongxinLiu / EasyAmplicon
  Easy Amplicon data analysis pipeline
  ☆271Updated 2 months ago
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆353Updated 5 months ago
• qiime2 / qiime2
  Official repository for the QIIME 2 framework.
  ☆483Updated this week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆215Updated 3 years ago
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆190Updated this week
• YuLab-SMU / MicrobiotaProcess
  A comprehensive R package for deep mining microbiome
  ☆184Updated 2 months ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆297Updated 5 months ago