edna

There are 0 repository under edna topic.

• nf-core / ampliseq

  Amplicon sequencing analysis workflow using DADA2 and QIIME2

  amplicon-sequencing16snf-corenextflowpipelineworkflowmetagenomicsrrna18sitsmetabarcodingqiime2ednataxonomic-classificationilluminaiontorrentmicrobiomepacbiotaxonomic-profiling
  Language:Nextflow 157

• terrimporter / CO1Classifier

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

  assignmentbayesianclassificationclassifierco1coiednametabarcodingmtdnanaivetaxonomic
  29

• TillMacher / TaxonTableTools

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

  dna-metabarcodinggraphical-user-interfacebiological-data-analysisotu-tablemetabarcoding-databiodiversitybioinformaticsbiomonitoringednaotusgraphical-interface
  Language:Python 21

• aomlomics / mitohelper

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

  noaa-omics-softwareednafish-edna-studiesmitofishmifish
  Language:Python 17

• billzt / MiFish

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

  ednaedna-pipeline
  Language:Python 13

• metabaRfactory / metabaR

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

  ednametabarcodingr-packagedata-cleaningbioinformatics-pipelineedna-pipeline
  Language:HTML 13

• bensutherland / eDNA_metabarcoding

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

  ednametabarcoding
  Language:R 10

• ifremer-bioinformatics / samba

  Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

  16s18smetabarcodingworkflowpipelinerrnanextflowedna
  Language:Nextflow 10

• 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.

  de-identificationdecontaminationednafastqfilterlong-readsmetabarcodingmetagenomicsmicrobiomenanoporenextflownf-corepipelineshort-readsshotguntaxonomic-classificationtaxonomic-profilingworkflow
  Language:Nextflow 9

• utopiaio / Mantis-Toboggan

  unofficial Edna Mall showtime API

  javascriptednanodejs
  Language:JavaScript 4

• 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

  ednalakesmetabarcoding
  Language:R 3

• walterxie / eDNA-pipeline

  eDNA pipeline

  metagenomicsednaredna-pipelinebiodiversity
  Language:R 3

• AnneSoBen / obitools_workflow

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

  ednametabarcodingbioinformatics-pipelineedna-pipeline
  Language:Python 2

• boopsboops / spider

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

  dna-barcodespecies-delimitationrednaspecies-identityevolution
  Language:R 2

• lyy005 / epps_nf

  eDNA pipeline showcase

  ednametabarcodingpipelinenextflow
  Language:Roff 2

• metabaRfactory / metabaR_external_data

  repository of data examples for the R package metabaR

  ednametabarcodingr-packagedata-cleaningbioinformatics-pipelineedna-pipelinedataset
  2

• walterxie / ComMA

  Community Matrix Analysis

  rednacommunity-matrix-analysisbiodiversity
  Language:HTML 2

• Clare-eDNA / eDNA_reflects_common_variation

  Environmental DNA reflects common mitochondrial haplotypic variation

  abaloneednaenvironmentaldnapauapopulationgenetics
  Language:R 1

• Grelot / bioinfo_singularity_recipes

  A collection of singularity recipies for bioinformatic pipelines.

  singularity-containerssingularitysingularity-hubsingularity-containerobitoolsrednametabarcodingbioinformatics
  Language:Shell 1

• 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

  supplementary-dataworkflowillumina-datafiltrationedna
  Language:R 1

• meghanmshea / intertidal-eDNA

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

  dnaednaenvironmentalintertidalmetabarcodingspatio-temporalspatiotemporal
  Language:HTML 1

• oliviergimenez / otterconnect

  website of the otterconnect project

  connectivityednaeuropean-otterlutra-lutrasite-occupancysocial-sciencesspatial-capture-recapturestatistical-ecology
  Language:HTML 1

• 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).

  bioinformaticsednametabarcodingsequence-analysistaxonomic-analysis
  Language:Python 0

• 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"

  ednamaximum-likelihoodmetabarcodingphylogenetic-placement
  Language:R 0

• manu-script / TaxDivToL

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

  ednametagenomics
  Language:Python 0

• maxfarrell / eDNAcamtrap

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

  cameratrapednametabarcoding
  Language:R 0

• OIMA-SeMMAP / Repo

  Home of all SeMMAP data

  dnadna-sequencingednaenvironmental
  0

• S-Myles / QIIME-2-plots

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

  amplicon-sequencingdata-visualizationdiversity-measuresednametabarcoding
  Language:R 0

• utopiaio / Gus-Petch

  iOS app for showtime. Built with React and WkWebView

  ednareactwkwebview
  Language:JavaScript 0

• YSKoseki / gmmDenoise

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

  bioinformaticsdenoisingednametabarcodingasvshaplotypes
  Language:R 0

• 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)

  ednajupyter-notebookphylogenetics
  Language:Jupyter Notebook

• dominiquefastus / AlphaFoldPipeline-ALFOtask

  In this research 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.

  alphafold2bioinformatics-pipelinecrystallographymachine-learningmolecular-replacementpredictionprotein-structurepythonstructural-biologyhpc-clustersednaslurm-workload-manager
  Language:Python

• EcoDynIZW / Axtner_2019_GigaScience

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

  metabarcodingidnaedna
  Language:Shell