amplicon-sequencing
There are 1 repository under amplicon-sequencing topic.
- Language:Nextflow 157
- ivar
andersen-lab / ivar
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
Language:C++ 114 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 101KasperSkytte / ampvis2
Tools for visualising microbial community amplicon data
Language:R 65gear-genomics / dicey
In-silico PCR, primer design and padlock design for in-situ sequencing
Language:C++ 41- Language:R 40
cafferychen777 / MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Language:R 24ngthomas / microhaplot
microhaplotype visualizer and analyzer
Language:Perl 18- Language:R 17
treangenlab / Olivar
Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing
Language:Python 14Aveglia / vAMPirus
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
Language:Nextflow 9yoann-dufresne / SLIM
A web app for environmental DNA metabarcoding analysis
Language:JavaScript 9RIVM-bioinformatics / AmpliGone
A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
Language:Python 8- Language:Jupyter Notebook 7
kohyamat / massgenotyping
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
Language:Python 7will-rowe / artic-tools
a set of tools for viral amplicon schemes
Language:C++ 6erictleung / shinydiversity
Interactive application to explore various ecological diversity metrics
Language:R 5abhijeetsingh1704 / AcetoScan
AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing
Language:Shell 4biomarv / 16S-rRNA-gene-analysis-using-QIIME2
QIIME2 worklflow. From raw data to a feature table.
mikemc / mgs-bias-manuscript
Analysis for McLaren, Willis, and Callahan (2019)
Language:R 4:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
Language:R 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 3eastmallingresearch / Metabarcoding_pipeline
Metabarcoding pipeline
Language:R 2marius44 / mothur_protocols
Repositorio de pipelines necesarios para analizar secuencias de amplicones illumina con mothur. Se incluyen análisis con asv de bacterias y de hongos (estos últimos poco explicados por Schloss en su SOP).
Language:R 2ryandkuster / readsynth
metagenome simulation for targeted and reduced-representation sequencing
Language:Shell 2aomlomics / erie
Study of cyanobacterial harmful algal blooms in Lake Erie using autonomous sampling and DNA sequencing
Language:HTML 1csc-training / chipster-microbial
Microbial Community Analysis with Chipster
GTseq / GTseek_utils
Utilities for analysis of multiplex amplicon sequencing data
Language:Perl 1johannabosch / Microbiome-Analysis-Using-Clusters
This is a 16S amplicon analysis for visualizing microbiome data using QIIME, QIIME2R and Phyloseq. DNA was isolated fom both sediment cores and seabird fecal samples for this analysis.
Language:CSS 1kevin-wamae / PlasmoSeq-DualTech
A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries
Language:Python 1PombertLab / ID16S
This pipeline reconstructs the composition of species from 16S amplicon sequencing datasets.
Language:Perl 1digo4 / Metagenomics
Here we discuss strategies and workflows to analyse metagenomics datasets
0hsmurali / Transitive_Annotation
The impact of transitive annotation on the training of taxonomic classifiers
Language:Jupyter Notebook 0muzafferarikan / gNOMO2
gNOMO2 allows integrated multi-omics analyses of microbiomes
Language:Python
