amplicon-sequencing
There are 68 repositories under amplicon-sequencing topic.
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
andersen-lab/ivar
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
microsud/Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
grimmlab/MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
KasperSkytte/ampvis2
Tools for visualising microbial community amplicon data
gear-genomics/dicey
In-silico PCR, primer design and padlock design for in-situ sequencing
Russel88/MicEco
Various functions for analysis of microbial community data
cafferychen777/MicrobiomeStat
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
treangenlab/Olivar
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
mikemc/metacal
Metagenomics calibration R package
ngthomas/microhaplot
microhaplotype visualizer and analyzer
adrientaudiere/MiscMetabar
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
flefler/CyanoSeq
CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing
RIVM-bioinformatics/AmpliGone
A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment
muzafferarikan/gNOMO2
gNOMO2 allows integrated multi-omics analyses of microbiomes
Aveglia/vAMPirus
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
mghotbi/DspikeIn
The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package
yoann-dufresne/SLIM
A web app for environmental DNA metabarcoding analysis
hsmurali/SCRAPT
SCRAPT: An Iterative Algorithm for Clustering Large 16S rRNA Gene Datasets
kohyamat/massgenotyping
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
biomarv/16S-rRNA-gene-analysis-using-QIIME2
QIIME2 worklflow. From raw data to a feature table.
will-rowe/artic-tools
a set of tools for viral amplicon schemes
erictleung/shinydiversity
Interactive application to explore various ecological diversity metrics
ImagoXV/NanoASV
NanoASV official repo
abhijeetsingh1704/AcetoScan
AcetoScan - Automated pipeline for the unsupervised analysis of FTHFS amplicon sequencing
mikemc/mgs-bias-manuscript
Analysis for McLaren, Willis, and Callahan (2019)
erictleung/dada2HPCPipe
:ocean: 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
tianrenmao/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.
eastmallingresearch/Metabarcoding_pipeline
Metabarcoding pipeline
GTseq/GTseek_utils
Utilities for analysis of multiplex amplicon sequencing data
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.
johannabosch/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.
marius44/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).
ryandkuster/readsynth
metagenome simulation for targeted and reduced-representation sequencing
AstraBert/AmpliPiper-docs
Docs for AmpliPiper, developed by @nhmvienna
treangenlab/InfA-amplicon
Amplicon sequencing of influenza A