Steinegger Lab Datasets

Tutorials

• ColabFold Tutorial by Ovchinnikov S, Mirdita M and Steinegger M
  
• ColabFold User Guide by Mirdita M and Ovchinnikov S
  
• Foldseek User Guide by Mirdita M and Steinegger M
  

Tools & Applications

• ColabFold Google Colab Notebook by Ovchinnikov S, Mirdita M and Steinegger M
  
• Foldseek Search Server by van Kempen M, Kim S, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, et al.
  
• Run ColabFold on your local computer by Moriwaki Y
  

Publications

• ColabFold: Making protein folding accessible to all by Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S and Steinegger M
  
• Fast and accurate protein structure search with Foldseek by van Kempen M, Kim S, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, et al.
  
• MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets by Steinegger M and Söding J
  

Logan Unitigs and Contigs of the Sequence Read Archive (SRA) on AWS

Tutorials

• Downloading unitigs of several accessions by Rayan Chikhi
  
• Downloading, mapping many contigs to a gene of interest by Rayan Chikhi
  
• Search for sequences inside unitigs or contigs by Rayan Chikhi
  

Tools & Applications

• f2sz by Anton Korobeynikov
  
• Logan Search by Pierre Peterlongo
  
• Minia 3 by Rayan Chikhi
  
• Open Virome by Artem Babaian
  

Publications

• Logan - Planetary-Scale Genome Assembly Surveys Life’s Diversity by Chikhi R., Lemane T., Loll-Krippleber R., et al (2025)
  

BUSCO Datasets

Tutorials

• BUSCO - from QC to gene prediction and phylogenomics by Matthew Berkeley
  

Publications

• BUSCO - assessing genomic data quality and beyond. by Mosè Manni, Matthew R. Berkeley, Mathieu Seppey, Evgeny M. Zdobnov
  
• BUSCO Update - Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. by Mosè Manni, Matthew R Berkeley, Mathieu Seppey, Felipe A Simão, Evgeny M Zdobnov
  
• OrthoDB and BUSCO update - annotation of orthologs with wider sampling of genomes. by Fredrik Tegenfeldt, Dmitry Kuznetsov, Mosè Manni, Matthew Berkeley, Evgeny M Zdobnov, Evgenia V Kriventseva
  

Kraken2 NCBI RefSeq Complete V205 database on AWS

Tutorials

• Using an Amazon Machine Image for analysing samples with Kraken2 by Robyn Wright
  Amazon EC2

Tools & Applications

• Kraken2 by Derrick Wood, Jennifer Lu and Ben Langmead
  

Publications

• From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools by Robyn J. Wright, Andre M. Comeau and Morgan G.I. Langille
  

QIIME 2 Tutorial Data

Tutorials

• Developing with QIIME 2 by Caporaso and Bolyen
  
• QIIME 2 User Documentation (currently being replaced by *Using QIIME 2*) by The QIIME 2 Development Team
  
• Using QIIME 2 by Caporaso Lab
  

The Human Microbiome Project

Publications

• New microbe genomic variants in patients fecal community following surgical disruption of the upper human gastrointestinal tract by Ranjit Kumar, Jayleen Grams, Daniel I. Chu, David K.Crossman, Richard Stahl, Peter Eipers, et al
  
• Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, et al.
  
• The Human Microbiome Project by Peter J. Turnbaugh, Ruth E. Ley, Micah Hamady, Claire M. Fraser-Liggett, Rob Knight & Jeffrey I. Gordon
  

run_dbcan CAZyme and CGC annotation database on AWS

Tutorials

• run_dbcan Documentation by Xinpeng Zhang; Haidong Yi; Yanbin Yin
  

Tools & Applications

• run_dbcan by Xinpeng Zhang; Haidong Yi; Jinfang Zheng; Le Huang; Qiwei Ge; Yanbin Yin
  

Publications

• dbCAN3: automated carbohydrate-active enzyme and substrate annotation by Jinfang Zheng, Qiwei Ge, Yuchen Yan, Xinpeng Zhang, Le Huang, Yanbin Yin
  

Hecatomb Databases

Tutorials

• The Hecatomb Tutorial by Michael Roach
  

Publications

• No Evidence Known Viruses Play a Role in the Pathogenesis of Onchocerciasis-Associated Epilepsy. An Explorative Metagenomic Case-Control Study by Michael Roach,Adrian Cantu,Melissa Krizia Vieri,Matthew Cotten,Paul Kellam,My Phan,Lia van der Hoek,Michel Mandro,Floribert Tepage,Germain Mambandu,Gisele Musinya,Anne Laudisoit,Robert Colebunders,Robert Edwards, John L. Mokili
  

Indexes for Kaiju

Tutorials

• Quickstart Tutorial for downloading the index files and running Kaiju. by Peter Menzel
  

Publications

• Fast and sensitive taxonomic classification for metagenomics with Kaiju by Peter Menzel et al (2016)
  

Reference Indexes for krepp

Tutorials

• Tutorial for using krepp indexes for metagenomic sequence analysis. by Ali Osman Berk Sapci
  

Publications

• A k-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement. by Sapci et al. (2024)
  

MetaGraph Sequence Indexes

Tutorials

• Usage within AWS by Oleksandr Kulkov
  AWS CloudFormationAWS Step FunctionsAWS LambdaAWS BatchAmazon S3Amazon SNS

Tools & Applications

• CloudFormation stack with a Step Function for dataset queries via AWS Batch by Oleksandr Kulkov
  

Publications

• A global metagenomic map of urban microbiomes and antimicrobial resistance by Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KE, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, et al.
  

Metagenomic reference libraries for Slacken

Tutorials

• Classifying metagenomic samples on AWS ElasticMapReduce by Johan Nyström-Persson
  Amazon EC2Amazon EMRAmazon S3

Tools & Applications

• Slacken by Johan Nyström-Persson, Nishad Bapatdhar
  

Publications

• Precise and scalable metagenomic profiling with sample-tailored minimizer libraries by Johan Nyström-Persson, Nishad Bapatdhar and Samik Ghosh
  

SocialGene RefSeq Databases

Tutorials

• How to use SocialGene on AWS by Chase M. Clark
  Amazon EC2

Tools & Applications

• socialgene on pypi.python.org - python module for creating and interacting with SocialGene Neo4j databases by Chase M. Clark
  

Publications

• Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene. by C. M. Clark, J. C. Kwan