Super preliminary list, compiled November 2017
General introduction
Mike Lee wrote a great short tutorial to get even the most novice beginner up to speed. Highly recommended, at Happy Belly Bioinformatics.
• The fundamentals of working at the command line: bash basics
• Baseline bash commands worth having in your arsenal: Six glorious commands
• Some real-life examples of how I use bash everyday: Why is this all worth it?
16S rRNA tools
Microbiome Datasets Are Compositional: And This Is Not Optional – Gregory B Gloor – Frontiers in Microbiology – November 2017
A list of R environment based tools for 16S rRNA gene data exploration, statistical analysis and visualization – Sudarshan Shetty – August 2017
Tools for 16S rRNA gene sequences binning and analysis
Nephele: A cloud platform for simplified, standardized, and reproducible microbiome data analysis – Nick Weber – Bioinformatics – October 2017
Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome – March 2017
Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research – André M. Comeau – mSystems – January 2017
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses – Ben Callahan – F1000 Research – November 2016
DADA2: high-resolution sample inference from Illumina amplicon data – Benjamin J Callahan – Nature Methods – May 2016
Compositional data analysis of the microbiome: fundamentals, tools, and challenges – Matthew C.B.Tsilimigras – Annals of Epidemiology – May 2016
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible – Paul J. McMurdie, Susan Holmes – PLOS Computational Biology – April 2014
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data – Paul J. McMurdie, Susan Holmes – PLOS ONE – April 2013
QIIME allows analysis of high-throughput community sequencing data – JG Caporaso – Nature Methods – April 2010
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities – Patrick D Schloss – Applied and Environmental Microbiology – December 2009
UniFrac: a new phylogenetic method for comparing microbial communities – C Lozupone – Applied Environmental Microbiology – 2005
LEFSE
Metagenomics tools
Shotgun metagenomics sequencing data analysis bioinformatics software tools – Omics Tools
A short list of tools for shotgun metagenomics – Microsized Mind – Thomas Haverkamp – May 2016
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies – Anastasis Oulas – Bioinform Biol Insights – May 2015
Tutorial: Tools For Metagenomic Data Analysis – Vijay – 2012
Tools for metagenomic (shotgun) microbiome assembly
Microbial Metagenomics Mock Scenario-based Sample Simulation (M3S3) – Yair Motro – Clinical Microbiology and Infection – August 2017
Shotcleaner: A high-throughput and modular workflow to quality control shotgun metagenomic DNA sequence libraries – Thomas Sharpton – Github – July 2017
Velvet: algorithms for de novo short read assembly using de Bruijn graphs – Daniel Zerbino – Genome Res – 2008
Tools for metagenomic classification
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads – Thomas Petersen – May 2017
Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations – Aaron Y Lee – BMC Bioinformatics – 2016
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes – Stephen Nayfach – PLOS Computational Biology – November 2015
Kraken: ultrafast metagenomic sequence classification using exact alignments – Derrick E Wood – Genome Biology – March 2014
eggNOG v4.0: nested orthology inference across 3686 organisms – S Powell – Nucleic Acids Research – 2014
Fast gapped-read alignment with Bowtie 2 – Ben Langmead – Nature Methods – March 2012
MetaPhlAn: Metagenomic microbial community profiling using unique clade-specific marker genes – N Segata – Nature Methods – 2012
Prodigal: prokaryotic gene recognition and translation initiation site identification – Dough Hyatt – March 2010
KEGG: Kyoto encyclopedia of genes and genomes – H Ogata – Nucleic Acids Research – 1999
Tools for metagenomic pathway analysis
A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S Hahn – Scientific Data – April 2017
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases – Ron Caspi – Nucleic Acids Research – November 2013
Tools for viral sequence detection
Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral” – Martin Hölzer – Advances in Virus Research – September 2017