edna

There are 35 repositories under edna topic.

  • nf-core/ampliseq

    Amplicon sequencing analysis workflow using DADA2 and QIIME2

    Language:Nextflow182144338115

  • terrimporter/CO1Classifier

    This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.

    30654

  • TillMacher/TaxonTableTools

    TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data

    Language:Python21393

  • aomlomics/mitohelper

    Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies

    Language:Python17318

  • billzt/MiFish

    This is the command line version of MiFish pipeline. It can also be used with any other eDNA meta-barcoding primers

    Language:Python132143

  • metabaRfactory/metabaR

    metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.

    Language:HTML134243

  • nf-core/detaxizer

    A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxa to identify (and remove) are Homo and Homo sapiens. Removal is optional.

    Language:Nextflow1316334

  • ifremer-bioinformatics/samba

    Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

    Language:Nextflow12355

  • bensutherland/eDNA_metabarcoding

    Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)

    Language:R11382

  • AnneSoBen/obitools_workflow

    A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.

    Language:Python4252

  • utopiaio/Mantis-Toboggan

    unofficial Edna Mall showtime API

    Language:JavaScript43282

  • HullUni-bioinformatics/Li_et_al_2019_eDNA_fish_monitoring

    Data processing workflow and supplementary data for Li et al. 2019 - Ground-truthing of a fish-based environmental DNA metabarcoding method for assessing the quality of lakes

    Language:R3300

  • walterxie/eDNA-pipeline

    eDNA pipeline

    Language:R3310

  • boopsboops/spider

    Official GitHub repository for the R package "Species Identity and Evolution in R" (spider)

    Language:R2241

  • lyy005/epps_nf

    eDNA pipeline showcase

    Language:Roff2200

  • metabaRfactory/metabaR_external_data

    repository of data examples for the R package metabaR

    2300

  • walterxie/ComMA

    Community Matrix Analysis

    Language:HTML2201

  • CALeDNA/Anacapa

    Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).

    Language:Python1101

  • Clare-eDNA/eDNA_reflects_common_variation

    Environmental DNA reflects common mitochondrial haplotypic variation

    Language:R1100

  • Grelot/bioinfo_singularity_recipes

    A collection of singularity recipies for bioinformatic pipelines.

    Language:Shell1200

  • HullUni-bioinformatics/Li_et_al_2018_eDNA_filtration

    Data processing workflow and supplementary data for Li et al. 2018 - The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding

    Language:R1401

  • meghanmshea/intertidal-eDNA

    Data and R code for "Environmental DNA (eDNA) metabarcoding differentiates between micro-habitats within the rocky intertidal" (Shea & Boehm)

    Language:HTML1100

  • oliviergimenez/otterconnect

    website of the otterconnect project

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  • dominiquefastus/AlphaFoldPipeline-ALFOtask

    In this project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.

    Language:Python0200

  • fridalp/eutardigrade_eDNA

    Supplementary files for the paper "Environmental DNA metabarcoding of Danish soil samples reveals new insight into the hidden diversity of eutardigrades in Denmark"

    Language:R0100
  • STREAM

    giorgiastaffoni/STREAM

    Ballini & Staffoni et al. (submitted to Hydrobiologia) workflow

    Language:Python0100

  • manu-script/TaxDivToL

    Supporting codes for Manu et al., Ecological Indicators (2023). Deep sequencing of extracellular eDNA enables total biodiversity assessment of ecosystems

    Language:Python0200

  • maxfarrell/eDNAcamtrap

    Data & Code Supplement for "Environmental DNA as a management tool for tracking artificial waterhole use in savanna ecosystems"

    Language:R0100

  • OIMA-SeMMAP/Repo

    Home of all SeMMAP data

    0100

  • S-Myles/QIIME-2-plots

    Primer scripts to produce meaningful visualisations from pre-processed metabarcoding data

    Language:R0100

  • utopiaio/Gus-Petch

    iOS app for showtime. Built with React and WkWebView

    Language:JavaScript02170

  • YSKoseki/gmmDenoise

    A set of functions for filtering erroneous sequences in eDNA metabarcoding data

    Language:R0100

  • CALeDNA/TaxonListToOpenTreePhylogeny

    This is a Jupyter Notebook to make phylogenetic trees with the Open Tree of Life from a list of taxa such as those from Anacapa output (CALeDNA format)

    Language:Jupyter Notebook10

  • codecreatede/go-alignment-block-genotyper-eDNA

    desining block alignment geneotyper tags based on the whole genome alignment or gene alignment for phylogenomics

    Language:Go

  • EcoDynIZW/Axtner_2019_GigaScience

    "An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies"

    Language:Shell00