amplicon

There are 3 repositories under amplicon topic.

torognes / vsearch
Versatile open-source tool for microbiome analysis
metabarcoding metagenomics chimera bioinformatics fastq fasta microbiome amplicon sequence-alignment clustering search
Language:C++ 652
benjjneb / dada2
Accurate sample inference from amplicon data with single nucleotide resolution
microbiome bioinformatics bioconductor taxonomy amplicon metagenomics metabarcoding
Language:R 459
benjjneb / decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
microbiome bioinformatics contamination metagenomics amplicon metabarcoding
Language:R 143
lucapinello / CRISPResso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
crispr-analysis crispr-cas9 crispr cas9 ngs amplicon python docker
Language:Python 131
nf-core / viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
viral metagenomics amplicon assembly variant-calling illumina pipeline workflow nextflow nf-core covid-19 covid19 virus sars-cov-2 nanopore ont artic long-read-sequencing oxford-nanopore
Language:Nextflow 113
microsud / Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
microbiome-analysis microbial-communities microbiome-data amplicon-sequencing microbiota amplicon 16s-rrna metagenomics
Language:CSS 108
FOI-Bioinformatics / flextaxd
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 gtdb ganon kraken2 custom-taxonomy metagenomic-classification custom-database taxonomic-classification taxonomic-classifications centrifuge krakenuniq ncbi-database amplicon 16s
Language:Python 64
UPHL-BioNGS / Cecret
Reference-based consensus creation
bioinformatics nextflow sars-cov-2 amplicon monkeypox
Language:Nextflow 45
gear-genomics / dicey
In-silico PCR, primer design and padlock design for in-situ sequencing
gear-genomics pcr primer primer-design in-silico sanger-sequencing amplicon amplicon-sequencing padlock in-situ-sequencing
Language:C++ 43
microsud / microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
microbiome microbiome-analysis microbial-communities metagenomics amplicon sequencing 16s core-microbiome qc-pipeline
Language:R 32
mikessh / mageri
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
bioinformatics cancer umi variant mutation mapping amplicon exon ctdna
Language:Java 21
compmetagen / micca
micca - MICrobial Community Analysis
amplicon bioinformatics clustering metagenomics
Language:Python 20
pirovc / grimer
GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
amplicon bokeh contamination dashboard interactive-visualizations metagenomics microbiome visualization
Language:Python 20
tobiasrausch / lorax
A long-read analysis toolbox for cancer and population genomics
long-reads long-read-sequencing cancer-genomics genomics bioinformatics telomere amplicon
Language:C++ 19
chienchi / amplicon_coverage_plot
interactive barplot for amplicon sequencing
amplicon coverage genome
Language:HTML 13
adrientaudiere / MiscMetabar
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
ecology metabarcoding ngs-analysis package r amplicon amplicon-sequencing biodiversity-informatics illumina r-package visualization
Language:R 12
HuaZou / bioinformatics_pipeline
Bioinformatics Pipeline
snakemake data-analysis pipeline metagenomics amplicon rna-seq mirna-seq methylation tcga-data geo-data
Language:R 12
Aveglia / vAMPirus
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
nextflow nextflow-pipelines virus viruses amplicon-sequencing amplicon amplicon-pipeline
Language:Nextflow 9
gear-genomics / silica
In-silico PCR amplification on complete genomes
gear-genomics pcr in-silico primer-design primer sanger-sequencing amplicon
Language:JavaScript 9
adriaaula / dada2_guidelines
A repository with a general dada2 pipeline for amplicon processing
dada2 16s 18s amplicon
Language:R 8
metagenlab / zAMP
zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
snakemake pipeline metagenomics amplicon
Language:R 8
yanhui09 / laca
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
denoise nanopore amplicon long-read-sequencing
Language:Python 7
HKU-BAL / MegaPath
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data
ngs metagenomics taxonomic-classification amplicon filter
Language:Java 6
Nucleomics-VIB / InSilico_PCR
extract long read subsequences from a pair of primers
insilico-pcr bbmap-msa amplicon
Language:Shell 5
sebrauschert / OceanOmics-amplicon
A pipeline to analyse marine fish amplicon data
amplicon amplicon-pipeline bioinformatics bioinformatics-pipeline dada2
Language:R 4
bailey-lab / miplicorn
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
r mip amplicon
Language:R 3
pjtorres / 16S_amplicon_preprocessing_code
Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code
16s microbiome amplicon
Language:Jupyter Notebook 3
rwst / process-ubiome-16S
process raw reads from ubiome
bioinformatics rna-seq microbiome-analysis amplicon 16s-rrna taxonomic-classification microbiology
Language:Python 3
Arkadiy-Garber / Taxonsluice
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
otu amplicon contamination silva environmental
Language:Python 2
caltha
JasperBoom / caltha
A python package to process UMI tagged mixed amplicon metabarcoding data.
umi metabarcoding amplicon python vsearch
Language:Python 2
jfjlaros / tssv
Targeted characterisation of short structural variation.
amplicon edit-distance levenshtein counting alignment primers tandem-repeats
Language:Python 2
sabahzero / Puerto-Nuevo_Coastal-Microbial-Ecology_16S-18S-Workflow_UlHasan-etal
This is a microbial amplicon sequence (16S and 18S iTag) data and analyses pipeline corresponding to the manuscript, "Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California" for public benefit and usage.
microbiology sequence coastal ecosystem bacteria archaea eukaryotes statistics permanova anova taxonomy amplicon
2
yjiakang / amplicon
amplicon pipeline
amplicon pipeline qiime2
Language:Shell 2
myonaung / Probe-Maker
Probe-Maker is intended for design of hybridisation probes for Plasmodium falciparum for long-read amplicon sequencing.
algorithm amplicon bioinformatics sequencing
1
natmurad / amplicon16S
Analysis for amplicon data
16s amplicon metagenomics microbiome-workflow phyloseq qiime2
Language:Jupyter Notebook 1
yanhui09 / nart
A tool for Nanopore Amplicon Real-Time (NART) analysis.
amplicon nanopore-sequencing real-time
Language:Python 1

amplicon

torognes / vsearch

benjjneb / dada2

benjjneb / decontam

lucapinello / CRISPResso

nf-core / viralrecon

microsud / Tools-Microbiome-Analysis

FOI-Bioinformatics / flextaxd

UPHL-BioNGS / Cecret

gear-genomics / dicey

microsud / microbiomeutilities

mikessh / mageri

compmetagen / micca

pirovc / grimer

tobiasrausch / lorax

chienchi / amplicon_coverage_plot

adrientaudiere / MiscMetabar

HuaZou / bioinformatics_pipeline

Aveglia / vAMPirus

gear-genomics / silica

adriaaula / dada2_guidelines

metagenlab / zAMP

yanhui09 / laca

HKU-BAL / MegaPath

Nucleomics-VIB / InSilico_PCR

sebrauschert / OceanOmics-amplicon

bailey-lab / miplicorn

pjtorres / 16S_amplicon_preprocessing_code

rwst / process-ubiome-16S

Arkadiy-Garber / Taxonsluice

JasperBoom / caltha

jfjlaros / tssv

sabahzero / Puerto-Nuevo_Coastal-Microbial-Ecology_16S-18S-Workflow_UlHasan-etal

yjiakang / amplicon

myonaung / Probe-Maker

natmurad / amplicon16S

yanhui09 / nart