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metabarcodingHere are 176 public repositories matching this topic...Language: All
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Versatile open-source tool for microbiome analysis
search bioinformatics clustering metagenomics chimera fasta microbiome fastq metabarcoding amplicon sequence-alignment
Accurate sample inference from amplicon data with single nucleotide resolution
Amplicon sequencing analysis workflow using DADA2 and QIIME2
workflow pipeline nextflow metagenomics pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its 18s taxonomic-classification amplicon-sequencing qiime2 nf-core taxonomic-profiling metataxonomics
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
A robust and fast clustering method for amplicon-based studies
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
Protist Ribosomal Reference database (PR2) - SSU rRNA gene database
creating reference databases for amplicon sequencing
eDNA metabarcoding pipeline
R mased batch sequence downloader, with primer development and in silico evaluation capabilities
This repository contains CO1 reference sets that can be used with the RDP Classifier, BLAST, or SINTAX to classify COI metabarcode sequences.
A python package to query different databases of boldsystems.org
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
workflow nanopore pipeline nextflow shotgun filter metagenomics edna microbiome fastq metabarcoding long-reads taxonomic-classification de-identification nf-core short-reads taxonomic-profiling decontamination
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
visualization package r r-package biodiversity-informatics ecology illumina metabarcoding amplicon ngs-analysis amplicon-sequencing
metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
NanoASV official repo
docker open-source workflow bioinformatics snakemake nanopore end-to-end conda singularity bioinformatics-pipeline metabarcoding conda-environment asv amplicon-sequencing nanopore-sequencing snakemake-workflow nanopore-analysis-pipeline nanopore-reads nanopore-minion metabarcoding-pipeline
CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
metabarcoding taxonomy-assignment taxonomic-classification amplicon-datasets amplicon-sequencing cyanobacteria taxonomy-database
A pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio
Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
workflow benchmarking snakemake metagenomics metabarcoding placement taxonomic-classification phylogenetic-placement phylo-kmers
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