Alternatives and similar repositories for decontam

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

• microsud / Tools-Microbiome-Analysis
  A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
  ☆117Updated 2 years ago
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆172Updated this week
• picrust / picrust
  Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tes…
  ☆91Updated 4 months ago
• Zymo-Research / figaro
  An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
  ☆94Updated last year
• SchlossLab / MiSeq_WetLab_SOP
  ☆61Updated 6 years ago
• donovan-h-parks / STAMP
  Statistical Analysis of Metagenomic Profiles
  ☆94Updated 5 years ago
• grimmlab / MicrobiomeBestPracticeReview
  Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
  ☆122Updated last year
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆72Updated 2 years ago
• danknights / sourcetracker
  ☆79Updated 2 years ago
• scwatts / fastspar
  Rapid and scalable correlation estimation for compositional data
  ☆96Updated last year
• UMNFuN / FUNGuild
  FUNGuild: parsing OTUs into functional guilds
  ☆124Updated last year
• ParkinsonLab / Metatranscriptome-Workshop
  Metatranscriptomics Tutorial
  ☆66Updated 2 years ago
• colinbrislawn / unite-train
  🍄 Qiime2 ITS classifiers for the UNITE database
  ☆47Updated 4 months ago
• david-barnett / microViz
  R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
  ☆123Updated 4 months ago
• caitiecollins / treeWAS
  treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
  ☆106Updated 10 months ago
• cozygene / FEAST
  Fast expectation maximization for microbial source tracking
  ☆136Updated last year
• PacificBiosciences / HiFi-16S-workflow
  Nextflow pipeline to analyze PacBio HiFi full-length 16S data
  ☆88Updated 5 months ago
• zoecastillo / microbiomeExplorer
  The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or t…
  ☆72Updated 3 years ago
• biobakery / biobakery_workflows
  bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validate…
  ☆130Updated 2 months ago
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆174Updated last week
• nf-core / ampliseq
  Amplicon sequencing analysis workflow using DADA2 and QIIME2
  ☆230Updated last week
• caporaso-lab / sourcetracker2
  SourceTracker2
  ☆82Updated last year
• SegataLab / lefse
  ☆86Updated last year
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆33Updated last year
• jbisanz / qiime2R
  Import qiime2 artifacts to R
  ☆173Updated last year
• waldronlab / curatedMetagenomicData
  Curated Metagenomic Data of the Human Microbiome
  ☆145Updated 2 months ago
• B-UMMI / chewBBACA
  BSR-Based Allele Calling Algorithm
  ☆147Updated last week
• mgoeker / table2itol
  Generating iToL annotations from Spreadsheet or CSV files
  ☆107Updated 5 years ago
• bokulich-lab / RESCRIPt
  REference Sequence annotation and CuRatIon Pipeline
  ☆98Updated last month
• biobakery / Maaslin2
  MaAsLin2: Microbiome Multivariate Association with Linear Models
  ☆151Updated 2 weeks ago