Alternatives and similar repositories for MiFish

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

• mahsa-mousavi / eDNAFlow

  View on GitHub
  ☆22Feb 23, 2023Updated 2 years ago
• rogotoh / PMiFish

  View on GitHub
  ☆13Feb 22, 2024Updated last year
• genner-lab / meta-fish-lib

  View on GitHub
  A generalised, dynamic DNA reference library for metabarcoding of fishes
  ☆18Jan 23, 2026Updated 3 weeks ago
• aomlomics / mitohelper

  View on GitHub
  Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies
  ☆21Nov 14, 2025Updated 3 months ago
• gjeunen / reference_database_creator

  View on GitHub
  creating reference databases for amplicon sequencing
  ☆48Jan 13, 2026Updated last month
• tobiasgf / lulu

  View on GitHub
  r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
  ☆72Dec 21, 2023Updated 2 years ago
• seqeralabs / nf-dragen

  View on GitHub
  POC Nextflow pipeline to run Illumina DRAGEN software
  ☆14Aug 15, 2025Updated 5 months ago
• bensutherland / eDNA_metabarcoding

  View on GitHub
  Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
  ☆12Jul 6, 2022Updated 3 years ago
• meglecz / mkCOInr

  View on GitHub
  Make a non-redundant, comprehensive COI database from NCBI and BOLD and include customizing options
  ☆16May 26, 2025Updated 8 months ago
• bokulich-lab / RESCRIPt

  View on GitHub
  REference Sequence annotation and CuRatIon Pipeline
  ☆98Updated this week
• donaldtmcknight / microDecon

  View on GitHub
  An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing
  ☆21Oct 17, 2023Updated 2 years ago
• HullUni-bioinformatics / metaBEAT

  View on GitHub
  Metabarcoding analyses pipeline - metaBarcoding and Environmental DNA Analysis Tool
  ☆20Apr 17, 2019Updated 6 years ago
• 2015qyliang / Numerical_Ecology_with_R-Second

  View on GitHub
  Making notes during study 'Numerical Ecology with R second edition'
  ☆24Aug 9, 2019Updated 6 years ago
• Linwei-Wu / warming_soil_biodiversity

  View on GitHub
  ☆24Jun 13, 2022Updated 3 years ago
• IUCNN / IUCNN

  View on GitHub
  Train neural networks based on geographic species occurrences, environmental data and existing IUCN Red List assessments to predict the …
  ☆28Updated this week
• krabberod / BIO9905MERG1_V21

  View on GitHub
  BIO9905MERG1 – Bioinformatics for Environmental Sequencing (DNA metabarcoding)
  ☆11Apr 9, 2023Updated 2 years ago
• DataBiosphere / data-portal

  View on GitHub
  ☆10Jan 26, 2026Updated 2 weeks ago
• AMBarbosa / ecotrends

  View on GitHub
  Spatio-temporal trends in habitat suitability from ecological niche models
  ☆14Feb 4, 2026Updated last week
• nf-core / readsimulator

  View on GitHub
  A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.
  ☆33Jun 3, 2025Updated 8 months ago
• enormandeau / barque

  View on GitHub
  eDNA metabarcoding pipeline
  ☆44Jan 22, 2026Updated 3 weeks ago
• tzhang-edu / GOWT

  View on GitHub
  ☆12Apr 8, 2021Updated 4 years ago
• ahoarfrost / fastBio

  View on GitHub
  Deep learning library for biological sequences. Extension of Fastai and Pytorch.
  ☆39May 30, 2025Updated 8 months ago
• ZhijianZhou01 / virusrecom

  View on GitHub
  Detecting recombination of viral lineages
  ☆11Dec 23, 2025Updated last month
• linancn / tiangong-lca-next

  View on GitHub
  TianGong-LCA-NEXT
  ☆19Updated this week
• ucsd-ccbb / C-VIEW

  View on GitHub
  This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens…
  ☆11Aug 1, 2023Updated 2 years ago
• EESI / microbiome_embeddings

  View on GitHub
  ☆10Feb 21, 2020Updated 5 years ago
• QuKunLab / COVID-19

  View on GitHub
  The R/Python scripts for the analysis of single-cell RNA-seq data from COVID-19 patients
  ☆10Dec 16, 2020Updated 5 years ago
• Squalomix / info

  View on GitHub
  Shark genomics & beyond - This is a central portal page for the project Squalomix, directed mainly by Molecular Life History Laboratory a…
  ☆11Aug 15, 2025Updated 5 months ago
• lsaravia / multiweb

  View on GitHub
  R package for Ecological Networks utility functions and metrics
  ☆10Dec 18, 2025Updated last month
• BorchLab / immApex

  View on GitHub
  Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning
  ☆12Feb 6, 2026Updated last week
• nleguillarme / taxonerd

  View on GitHub
  TaxoNERD : recognizing taxonomic entities using deep models
  ☆45Jun 12, 2024Updated last year
• valentinitnelav / valentinitnelav.github.io

  View on GitHub
  I do not have time to maintain this anymore! It remains as a sandbox/playground :)
  ☆11May 13, 2024Updated last year
• Martinez-Gregorio-Hector / workflow_to_analysis_WES

  View on GitHub
  workflow to analysis of whole-exome-sequencing
  ☆12Feb 12, 2020Updated 6 years ago
• veg / datamonkey-js

  View on GitHub
  Datamonkey - Run state-of-the-art statistical models through the comfort of your browser
  ☆10Updated this week
• qbic-pipelines / vcftomaf

  View on GitHub
  Nextflow pipeline to convert VCF files into MAF files.
  ☆10Dec 12, 2025Updated 2 months ago
• Dishantkharkar / 100_Days_OF_Python

  View on GitHub
  This repository chronicles my 100-day Python learning journey, where I'll start from the very basics and work my way up to more advanced …
  ☆13Feb 9, 2024Updated 2 years ago
• abdenlab / ipylangchat

  View on GitHub
  Simple Jupyter chat UI for LangChain
  ☆11Jul 3, 2024Updated last year
• ChengGaoBerkeley / EPICON.Mycobiome

  View on GitHub
  ☆13Jun 1, 2021Updated 4 years ago
• tudorgroza / fast_hpo_cr

  View on GitHub
  ☆15May 19, 2025Updated 8 months ago