Alternatives and similar repositories for PMiFish

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

• Russel88 / MicEco
  Various functions for analysis of microbial community data
  ☆44Updated 2 years ago
• tobiasgf / lulu
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆66Updated last year
• jcmcnch / eASV-pipeline-for-515Y-926R
  This is a collection of scripts for analyzing mixed 16S/18S amplicon sequences using tools such as qiime2, DADA2, deblur, and bbtools
  ☆31Updated 4 months ago
• GuillemSalazar / EcolUtils
  Utilities for community ecology analysis
  ☆18Updated 4 years ago
• mahsa-mousavi / eDNAFlow
  ☆21Updated 2 years ago
• metabaRfactory / metabaR
  metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
  ☆15Updated 4 months ago
• uit-metabarcoding / MJOLNIR
  MJOLNIR Metabarcoding Joining Obitools & Linkage Networks In R
  ☆18Updated 11 months ago
• MadsAlbertsen / ampvis
  [deprecated] Please use ampvis2
  ☆8Updated 7 years ago
• tao-bioinfo / MiFish
  This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers
  ☆20Updated last year
• stegen / Stegen_etal_ISME_2013
  Code for running analyses carried out in Stegen et al. 2013, ISME
  ☆29Updated 7 years ago
• donaldtmcknight / microDecon
  An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing
  ☆16Updated last year
• Russel88 / DOC
  Dissimilarity Overlap Curve analysis
  ☆11Updated 2 years ago
• ChengGaoBerkeley / EPICON.Mycobiome
  ☆13Updated 4 years ago
• gjeunen / reference_database_creator
  creating reference databases for amplicon sequencing
  ☆38Updated 2 months ago
• bulksoil / BioProtocol
  Repo for a Microbiome Protocol
  ☆10Updated 7 years ago
• moyn413 / nifHdada2
  dada2 formatted nifH database
  ☆11Updated last year
• terrimporter / CO1Classifier
  This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequen…
  ☆32Updated 2 years ago
• mahendra-mariadassou / phyloseq-extended
  Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" p…
  ☆33Updated 3 months ago
• genner-lab / meta-fish-lib
  A generalised, dynamic DNA reference library for metabarcoding of fishes
  ☆16Updated 9 months ago
• aomlomics / mitohelper
  Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies
  ☆19Updated 2 months ago
• ChiLiubio / file2meco
  Transform files to the microtable object with microeco package
  ☆27Updated 2 months ago
• ErnakovichLab / dada2_ernakovichlab
  ☆16Updated this week
• eukref / pipeline
  EukRef curation pipeline
  ☆13Updated 4 years ago
• ryanjw / co-occurrence
  R scripts for performing co-occurrence analyses
  ☆34Updated 10 years ago
• gmteunisse / fantaxtic
  Fantaxtic - Nested Bar Plots for Phyloseq Data
  ☆30Updated 10 months ago
• frederic-mahe / swarm
  A robust and fast clustering method for amplicon-based studies
  ☆31Updated 2 years ago
• VascoElbrecht / JAMP
  JAMP - Just Another Metabarcoding Pipeline
  ☆35Updated 3 years ago
• danknights / sourcetracker
  ☆74Updated last year
• yoann-dufresne / SLIM
  A web app for environmental DNA metabarcoding analysis
  ☆10Updated 3 years ago
• agmcfarland / r_phylogenetics_worshop
  Using ggtree to build phylogenetic trees
  ☆47Updated 7 months ago