This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers
☆22Jul 23, 2025Updated last year
Alternatives and similar repositories for MiFish
Users that are interested in MiFish are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆24Feb 23, 2023Updated 3 years ago
- ☆12Aug 6, 2026Updated 3 weeks ago
- Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies☆21Jul 12, 2026Updated last month
- A generalised, dynamic DNA reference library for metabarcoding of fishes☆19Aug 20, 2026Updated last week
- Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)☆12Jul 6, 2022Updated 4 years ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- creating reference databases for amplicon sequencing☆52Jan 13, 2026Updated 7 months ago
- Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@…☆48Jan 18, 2024Updated 2 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆75Dec 21, 2023Updated 2 years ago
- POC Nextflow pipeline to run Illumina DRAGEN software☆14Aug 15, 2025Updated last year
- Make a non-redundant, comprehensive COI database from NCBI and BOLD and include customizing options☆20May 26, 2025Updated last year
- An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing☆21Oct 17, 2023Updated 2 years ago
- REference Sequence annotation and CuRatIon Pipeline☆101Jul 21, 2026Updated last month
- Making notes during study 'Numerical Ecology with R second edition'☆25Aug 9, 2019Updated 7 years ago
- Train neural networks based on geographic species occurrences, environmental data and existing IUCN Red List assessments to predict the …☆28Jul 8, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- snpick is a fast and memory-efficient Rust-based SNP extraction tool designed to handle large genomic alignments with minimal RAM usage a…☆17Aug 22, 2026Updated last week
- ☆17Jul 15, 2026Updated last month
- ☆26Jun 13, 2022Updated 4 years ago
- Metabarcoding analyses pipeline - metaBarcoding and Environmental DNA Analysis Tool☆20Apr 17, 2019Updated 7 years ago
- eDNA metabarcoding pipeline☆48Jul 22, 2026Updated last month
- This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens…☆11Aug 1, 2023Updated 3 years ago
- ☆12Apr 8, 2021Updated 5 years ago
- A high-performance in-silico PCR tool for primer matching and product extraction from FASTA and GenBank sequences.☆18Feb 25, 2026Updated 6 months ago
- ☆15Apr 1, 2024Updated 2 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- 📦 R package to compute functional diversity indices efficiently☆44Aug 20, 2026Updated last week
- BIO9905MERG1 – Bioinformatics for Environmental Sequencing (DNA metabarcoding)☆11Apr 9, 2023Updated 3 years ago
- Spatio-temporal trends in habitat suitability from ecological niche models☆15Feb 4, 2026Updated 6 months ago
- A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.☆35Jul 28, 2026Updated last month
- GeneMiner2 is an enhanced version of our previous developments Easy353 and GeneMiner☆19Updated this week
- fork的一个repo,我主要用来放解决 Fcitx 在 RStudio 中中文输入的问题 lib 文件☆14Feb 20, 2026Updated 6 months ago
- GenBank taxonomy processing tools☆15Jun 30, 2018Updated 8 years ago
- I do not have time to maintain this anymore! It remains as a sandbox/playground :)☆11May 13, 2024Updated 2 years ago
- This is a read-only mirror of the CRAN R package repository. rgdal — Bindings for the 'Geospatial' Data Abstraction Library. Homepage: …☆13Jun 1, 2023Updated 3 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- EnDED is a program that aims to detect environmentally-driven ("indirect") edges in an association network.☆10Dec 1, 2023Updated 2 years ago
- Repository for all the code associated with the paper "Reconciling biodiversity protection, food production, and climate change mitigatio…☆19Oct 10, 2022Updated 3 years ago
- Repo for a Microbiome Protocol☆10Apr 26, 2018Updated 8 years ago
- Deep learning library for biological sequences. Extension of Fastai and Pytorch.☆39Jul 17, 2026Updated last month
- A metatranscriptomic pipeline optimized for the study of microeukaryotes.☆18Dec 30, 2025Updated 8 months ago
- R package for Ecological Networks utility functions and metrics☆11Aug 3, 2026Updated 3 weeks ago
- A book for my course☆26Updated this week