Software and Tools for Amplicon Metagenomics

WebApps/WebTools

1. Phylo.io
   • Description: Nice and clean web application for visualizing phylogenetic trees.
   • Link: http://phylo.io/
2. MicrobiomeAnalyst
   • Description: MicrobiomeAnalyst is a comprehensive statistical, visual and meta-analysis of microbiome data.
   • Link: https://www.microbiomeanalyst.ca

Software and Tools

1. QIIME2
   • Description: QIIME2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
   • Link: https://docs.qiime2.org/2019.7/install
2. mothur
   • Description: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data.
   • Link: https://github.com/mothur/mothur/releases/tag/v.1.43.0
3. KRAKEN
   • Description: Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences.
   • Link: http://ccb.jhu.edu/software/kraken
4. USEARCH
   • Description: USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
   • Link: https://www.drive5.com/usearch
5. VSEARCH
   • Description: VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool.
   • Link: https://github.com/torognes/vsearch
6. MG-RAST
   • Description: MG-RAST is an open source, open submission web application server that suggests automatic phylogenetic and functional analysis of metagenomes.
   • Link: https://www.mg-rast.org
7. PICRUSt
   • Description: PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
   • Link: http://picrust.github.io/picrust
8. pplacer
   • Description: Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
   • Link: https://matsen.fhcrc.org/pplacer
9. The Exelixis Lab [Curated Collection of Software/Tools]
   • Description: Include software/tools for:
   • Phylogenetic Inference
   • Phylogenetic Post-Analysis
   • Next Generation Sequencing & Sequence Analysis
   • Population genetics
   • Web services
   • etc.
   • Link: https://cme.h-its.org/exelixis/software.html

R packages

1. microbiome
   • Description: Tools for the exploration and analysis of microbiome profiling data sets, in particular large-scale population studies and 16S taxonomic profiling.
   • Tutorial: https://microbiome.github.io/tutorials
   • Link: https://github.com/microbiome/microbiome
2. microbiomeSeq
   • Description: An R package for microbial community analysis in an environmental context
   • Tutorial: http://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html
   • Link: https://github.com/umerijaz/microbiomeSeq
3. matR - Metagenomics Analysis Tools
   • Description: An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. Integrates easily with other R packages and non-R software.
   • Tutorial: https://www.mcs.anl.gov/~braithwaite/matR/docs-and-pubs/matR-user-manual.pdf
   • Link: https://rdrr.io/cran/matR
4. MonoPhy
   • Description: The R package MonoPhy allows assessment and exploration of monophyly of taxa in a phylogeny.
   • Tutorial: https://cran.r-project.org/web/packages/MonoPhy/vignettes/MonoPhyVignette.html
   • Link: https://cran.r-project.org/web/packages/MonoPhy/index.html