Bioinformatics tools paper collection

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



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