Versatile open-source tool for microbiome analysis

Accurate sample inference from amplicon data with single nucleotide resolution

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

Assembly and intrahost/low-frequency variant calling for viral samples

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

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.

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

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

R package MiscMetabar: Miscellaneous functions for metabarcoding analysis

micca - MICrobial Community Analysis

interactive barplot for amplicon sequencing

Bioinformatics Pipeline

In-silico PCR amplification on complete genomes

A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)

A repository with a general dada2 pipeline for amplicon processing

Automated virus amplicon sequencing analysis program integrated with Nextflow pipeline manager.

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

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

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.

Long-read haplotyping of small sequences with SNP-encoded de Bruijn graphs

Some tools made along the way when analyzing 16S amplicon data and metagenomics processing code

amplicon pipeline