There are 3 repositories under amplicon topic.
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
Assembly and intrahost/low-frequency variant calling for viral samples
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
Reference-based consensus creation
In-silico PCR, primer design and padlock design for in-situ sequencing
The is mostly a wrapper tool using phyloseq and microbiome R packages.
MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers
GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.
A long-read analysis toolbox for cancer and population genomics
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
Bioinformatics Pipeline
Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.
In-silico PCR amplification on complete genomes
A repository with a general dada2 pipeline for amplicon processing
zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data
extract long read subsequences from a pair of primers
A pipeline to analyse marine fish amplicon data
A unified framework for molecular inversion probe and amplicon analysis. Provides the tools to parse, manipulate, analyze, and visualize data.
Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code
process raw reads from ubiome
Reference-based, heuristic algorithm for identification of potential contaminants in mothur-formatted OTU tables
A python package to process UMI tagged mixed amplicon metabarcoding data.
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.
Probe-Maker is intended for design of hybridisation probes for Plasmodium falciparum for long-read amplicon sequencing.
Analysis for amplicon data