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
R package MiscMetabar: Miscellaneous functions for metabarcoding analysis
micca - MICrobial Community Analysis
Bioinformatics Pipeline
In-silico PCR amplification on complete genomes
A reproducible and scalable workflow for Long Amplicon Consensus Analysis (LACA)
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