16s

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Here are 74 public repositories matching this topic...

nf-core / ampliseq

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Amplicon sequencing analysis workflow using DADA2 and QIIME2

workflow pipeline nextflow metagenomics 16s qiime rrna amplicon-sequencing nf-core

Updated Sep 15, 2022
Nextflow

FOI-Bioinformatics / flextaxd

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FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

ncbi-taxonomy taxonomic-classifications amplicon 16s ncbi-database custom-taxonomy custom-database metagenomic-classification centrifuge taxonomic-classification kraken2 gtdb ganon krakenuniq

Updated Jul 13, 2022
Python

rdpstaff / RDPTools

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Collection of commonly used RDP Tools for easy building

bioinformatics microbiology microbiome bayesian-classifiers 16s sequence-alignment

Updated Dec 30, 2020
Makefile

Russel88 / DAtest

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Compare different differential abundance and expression methods

metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods

Updated Mar 8, 2022
R

epruesse / SINA

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SINA - Reference based multiple sequence alignment

bioinformatics alignment sequence 16s rrna silva

Updated Dec 13, 2020
C++

microsud / microbiomeutilities

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The is mostly a wrapper tool using phyloseq and microbiome R packages.

sequencing metagenomics microbial-communities microbiome amplicon 16s microbiome-analysis core-microbiome qc-pipeline

Updated Apr 14, 2021
R

Russel88 / MicEco

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Various functions for analysis of microbial community data

microbial-communities microbiome 16s microbiome-analysis microbial-ecology amplicon-sequencing null-model

Updated Aug 5, 2022
R

shandley / Microbiome-Analysis-Using-R

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Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

teaching microbiome 16s phyloseq dada2

Updated Aug 24, 2022
HTML

pnnl / hundo

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💯 Snakemake-based amplicon processing protocol for 16S and ITS sequences.

metagenomics 16s

Updated Aug 8, 2019
HTML

ycl6 / 16S-rDNA-V3-V4

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16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

bioinformatics microbiome illumina 16s microbiota phyloseq dada2 lefse picrust2

Updated Jul 19, 2021
R

tmbuza / iMAP

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iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

pipeline metagenomics profiling microbiome amplicon 16s rrna microbilal

Updated Sep 13, 2022
HTML

smdabdoub / phylotoast

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Tools for phylogenetic data analysis including visualization and cluster-computing support.

visualization python bioinformatics cross-platform hpc slurm computational-biology phylogenetics microbial-genomics microbiome 16s qiime pbs microbiome-analysis

Updated Dec 18, 2021
Python

itsmisterbrown / microfiltR

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accessory functions for processing microbial community data

microbiome 16s microbiome-analysis phyloseq 18s marker-gene-analysis

Updated Jun 27, 2019
R

ElDeveloper / dogs

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Companion notebooks for "Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks"

notebook ibd microbiome 16s qiime jupyer

Updated Jul 13, 2018
Jupyter Notebook

quadram-institute-bioscience / dadaist2

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Dadaist2 🟨 Highway to R

bioinformatics taxonomy metabarcoding 16s phyloseq dada2 asv amplicon-pipeline

Updated Aug 24, 2022
HTML

microgenlab / porefile

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A Nextflow full-length 16S profiling pipeline for ONT reads

docker nanopore pipeline nextflow singularity profiling 16s

Updated Mar 29, 2022
Nextflow

ohnosequences / db.rna16s

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A comprehensive, compact, and automatically curated 16S database

bioinformatics database rna16s bacteria 16s

Updated Nov 28, 2018
Scala

ifremer-bioinformatics / samba

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Standardized and Automated MetaBarcoding Analyses workflow (Mirror)

workflow pipeline nextflow edna metabarcoding 16s rrna 18s

Updated Sep 9, 2022
Nextflow

microUCPH / amplicon_data_analysis

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Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project

statistics data-analysis microbiome 16s taxonomic-classification dada2 amplicon-data-analysis

Updated May 25, 2022
HTML

GenomicaMicrob / OTUsamples2krona

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Simple script to generate Krona charts for all samples in an OTU table file

metagenomics 16s krona-charts

Updated Dec 7, 2018
Shell

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