amplicon
There are 55 repositories under amplicon topic.
torognes/vsearch
Versatile open-source tool for microbiome analysis
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
benjjneb/decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
lucapinello/CRISPResso
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
microsud/Tools-Microbiome-Analysis
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
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 )
UPHL-BioNGS/Cecret
Reference-based consensus creation
gear-genomics/dicey
In-silico PCR, primer design and padlock design for in-situ sequencing
microsud/microbiomeutilities
The is mostly a wrapper tool using phyloseq and microbiome R packages.
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.
mikessh/mageri
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
tobiasrausch/lorax
A long-read analysis toolbox for cancer and population genomics
compmetagen/micca
micca - MICrobial Community Analysis
adrientaudiere/MiscMetabar
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
chienchi/amplicon_coverage_plot
interactive barplot for amplicon sequencing
HuaZou/bioinformatics_pipeline
Bioinformatics Pipeline
adriaaula/dada2_guidelines
A repository with a general dada2 pipeline for amplicon processing
Aveglia/vAMPirus
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
gear-genomics/silica
In-silico PCR amplification on complete genomes
metagenlab/zAMP
zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
yanhui09/laca
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
HKU-BAL/MegaPath
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data
Nucleomics-VIB/InSilico_PCR
extract long read subsequences from a pair of primers
sebrauschert/OceanOmics-amplicon
A pipeline to analyse marine fish amplicon data
bailey-lab/miplicorn
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
bluenote-1577/dbghaplo
Long-read haplotyping of small sequences with SNP-encoded de Bruijn graphs
BostonGene/pyigmap
[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences
pjtorres/16S_amplicon_preprocessing_code
Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code
rwst/process-ubiome-16S
process raw reads from ubiome
yjiakang/amplicon
amplicon pipeline
Arkadiy-Garber/Taxonsluice
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
JasperBoom/caltha
A python package to process UMI tagged mixed amplicon metabarcoding data.
natmurad/amplicon16S
Analysis for amplicon data
robiwangriff/ENA-submission-in-R
R functions and workflow for submitting amplicon sequence data to the ENA.
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.