QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.

File formatting and conversion

USEARCH is a unique sequence analysis tool with thousands of users world-wide.

File formatting and conversion.

Versatile open-source tool for metagenomics.

R is a free software environment for statistical computing and graphics.

ITS sequences detection and filtering.

Database construction, database searching and sequence filtering.

Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Designed to be a general-use format for representing biological sample by observation contingency tables. 

Computational method that helps microbial ecologists to investigate concealed diversity within their operational taxonomic units at an extremely precise level by utilizing very subtle variations among 16S Ribosomal RNA gene sequences.

Data analyses and plotting.

Interactive data visualization and exploration.

Data analysis using network inference tools.

Interactive network visualization tool.

Genome assembler.

Genome assemblies evaluator.

Automated binning algorithm to recover genomes from multiple metagenomic datasets.

RStudio makes R easier to use. It includes a code editor, debugging & visualization tools.

- phyloseq: Import, share, and analyze microbiome census data using R.

- vegan: CRAN package for the analysis of ecological communities.

- ggplot2: Graphing package implemented on top of the R statistical package.

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Contig Integrator for Sequence Assembly.

Produces high quality microbial genome assemblies on a laptop computer without any parameter tuning.

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.