Topic: metabarcoding Goto Github
Some thing interesting about metabarcoding
Some thing interesting about metabarcoding
metabarcoding,R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
User: adrientaudiere
Home Page: https://adrientaudiere.github.io/MiscMetabar/
metabarcoding,Public repository of data and analyses from Dirks and Jackson (2020), "Community structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy", Applied and Environmental Microbiology 86 (19)
User: aldendirks
metabarcoding,Course material for the Action Nationale de Formation (ANF): Exploration de la diversité taxonomique des écosystèmes par metabarcoding
Organization: anf-metabiodiv
Home Page: https://ANF-MetaBioDiv.github.io/course-material/
metabarcoding,A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.
User: annesoben
metabarcoding,Accurate sample inference from amplicon data with single nucleotide resolution
User: benjjneb
Home Page: http://benjjneb.github.io/dada2/
metabarcoding,Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
User: benjjneb
Home Page: https://benjjneb.github.io/decontam/
metabarcoding,Pipeline to analyze eDNA metabarcoding samples (PE and SE, demultiplexed, multiplexed)
User: bensutherland
metabarcoding,A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
Organization: cvua-rrw
Home Page: https://cvua-rrw.github.io/FooDMe
metabarcoding,Retrieve sequences flanked by an arbitrary number of primers from a nucleotide collection.
Organization: cvua-rrw
metabarcoding,A web tool for optimally choosing eDNA primer pairs to identify a set of taxa.
User: davidlougheed
Home Page: https://snipe.dlougheed.com/
metabarcoding,A python package to query different databases of boldsystems.org
User: dominikbuchner
metabarcoding,A tool to select the best primers to perform quantitative metabarcoding studies.
User: dsoldevila
metabarcoding,eDNA metabarcoding pipeline
User: enormandeau
metabarcoding,CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
User: flefler
metabarcoding,A collection of singularity recipies for bioinformatic pipelines.
User: grelot
metabarcoding,Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
Organization: grunwaldlab
Home Page: http://grunwaldlab.github.io/metacoder_documentation
metabarcoding,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
Organization: hulluni-bioinformatics
metabarcoding,Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
Organization: ifremer-bioinformatics
Home Page: https://gitlab.ifremer.fr/bioinfo/SAMBA-nextflow
metabarcoding,NanoASV official repo
User: imagoxv
metabarcoding,A python package to process UMI tagged mixed amplicon metabarcoding data.
User: jasperboom
metabarcoding,metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
User: metabarfactory
Home Page: http://metabaRfactory.github.io/metabaR
metabarcoding,repository of data examples for the R package metabaR
User: metabarfactory
Home Page: http://metabaRfactory.github.io/metabaR
metabarcoding,A pipeline to create reference databases for arbitrary markers and taxonomic groups from NCBI data
Organization: molbiodiv
Home Page: https://bcdatabaser.molecular.eco
metabarcoding,Pipeline for building topologically-constrained phylogenies from DNA barcode data
Organization: naturalis
Home Page: https://naturalis.github.io/barcode-constrained-phylogeny/
metabarcoding,Amplicon sequencing analysis workflow using DADA2 and QIIME2
Organization: nf-core
Home Page: https://nf-co.re/ampliseq
metabarcoding,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.
Organization: nf-core
Home Page: https://nf-co.re/detaxizer
metabarcoding,
User: nunofonseca
metabarcoding,taxalogue - a toolkit to create comprehensive CO1 reference databases
User: nwnoll
metabarcoding,Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
Organization: phylo42
metabarcoding,Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences
Organization: phylo42
metabarcoding,Shiny application to access metaPR2 database
Organization: pr2database
metabarcoding,Scripts for paper Vaulot et al. 2022
Organization: pr2database
metabarcoding,Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
Organization: pr2database
metabarcoding,Dadaist2 🟨 Highway to R
Organization: quadram-institute-bioscience
Home Page: https://quadram-institute-bioscience.github.io/dadaist2/
metabarcoding,Code and plots for the paper of Jauss & Walden et al., 2020, https://www.frontiersin.org/articles/10.3389/fmicb.2020.592189/
User: rjauss
Home Page: https://www.frontiersin.org/articles/10.3389/fmicb.2020.592189/
metabarcoding,Trimming Sanger sequencing reads by quality
User: sam-k
metabarcoding,
Organization: sushilab
metabarcoding,Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
User: talitrus
Home Page: https://www.nature.com/articles/s41598-020-63565-9
metabarcoding,Qiime2 Artifact eXtractor
User: telatin
Home Page: https://telatin.github.io/qax/
metabarcoding,This repository contains 18S reference sets that can be used with the RDP Classifier to classify 18S rDNA metabarcode sequences.
User: terrimporter
metabarcoding,This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
User: terrimporter
metabarcoding,This repository contains the scripts used to retrieve and analyze the data reported in Porter & Hajibabaei 2018 bioRxiv doi: https://doi.org/10.1101/353904
User: terrimporter
metabarcoding,A robust and fast clustering method for amplicon-based studies
User: torognes
metabarcoding,Versatile open-source tool for microbiome analysis
User: torognes
metabarcoding,JAMP - Just Another Metabarcoding Pipeline
User: vascoelbrecht
metabarcoding,R mased batch sequence downloader, with primer development and in silico evaluation capabilities
User: vascoelbrecht
metabarcoding,Supplementary files for Ribeiro et al. ISME 2018
User: vaulot
metabarcoding,A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
User: vmikk
Home Page: https://next-its.github.io
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