16s-rrna
There are 3 repositories under 16s-rrna topic.
microsud / Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Language:CSS 109grimmlab / MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Language:Shell 101- ggpicrust2
cafferychen777 / ggpicrust2
Make Picrust2 Output Analysis and Visualization Easier
Language:R 85 Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Language:R 24- Language:Python 19
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Ebedthan / hyperex
Hypervariable region primer-based extractor for 16S rRNA and other SSU/LSU sequences.
Language:Rust 9ali-kishk / AmpliconNet
Sequence based 16S rRNA Taxonomic classifier using MLP
Language:Jupyter Notebook 8- Language:R 8
achillesrasquinha / 16SMaRT
16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).
Language:Python 7- Language:Jupyter Notebook 7
- speciateIT
ravel-lab / speciateIT
Fast, accurate taxonomic assignments for the human vaginal microbiota
Language:HTML 7 oschakoory / RiboTaxa
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
Language:Shell 6xapple / crest4
The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.
Language:Python 5biomarv / 16S-rRNA-gene-analysis-using-QIIME2
QIIME2 worklflow. From raw data to a feature table.
- Language:R 4
- Language:Shell 4
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
- Language:JavaScript 3
nlabrad / CIMS-Cyanobacterial-ITS-motif-slicer
A tool to identify and extract the commonly used ITS folding motifs from a 16s-23s rRNA sequence.
Language:Python 3SchlossLab / mothur-snakemake-workflow
Snakemake template for microbial amplicon sequence analysis with mothur.
Language:Python 3Shuyib / Phylogenetic-tree-study
Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7
Language:Jupyter Notebook 3tianrenmao / 16S-18S-ITS-ASAP
This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequences.
Language:Perl 3BCCDC-PHL / 16s-nf
Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.
Language:Python 2dschnei1 / ngs4ecoprod
NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis
Language:Shell 2IMCBioinformatics / dada2_snakemake_workflow
Amplicon sequencing workflow with snakemake and dada2
Language:R 2- MicrobioSee2
jinhuili-lab / MicrobioSee2
MicrobioSee2, a desktop sofware for visulization of microbiome result, which contian multiple modules, such as Alpha Diversity, Beta Diversity, Species Conpositions, volcano plot, and pie chart.
Language:HTML 2 NewtonLabUWM / Sewage_TimeSeries
Data and code for LaMartina et al., 2021
Language:R 2raymondkiu / bactspeciesID
Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies
Language:Shell 2rjstevick / NBayTNCoystersAnalysis
Scripts for analysis of metatranscriptomic and 16S rRNA amplicon data from wild oysters in Narragansett Bay
Language:R 2rwst / process-ubiome-16S
process raw reads from ubiome
Language:Python 2ahmedmoustafa / ALS
Analysis of the gut microbiome of Amyotrophic Lateral Sclerosis (ALS) patients using the DADA2 workflow
Language:Jupyter Notebook 1- Language:R 1
leahkemp / running_16S_rRNA_pipeline
Trying to help a colleague get a 16s-rRNA-Sanger snakemake pipeline working.
Data and code for Kimbell et al., 2021
Language:R 1The `pacmill` python package is a bioinformatics pipeline that is developed to process microbial 16S amplicon sequencing data and produce PDF reports detailing taxonomical assignments along with other statistics.
Language:Python 1
