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Title: Tutorials · soedinglab/MMseqs2 Wiki · GitHub

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Description: MMseqs2: ultra fast and sensitive search and clustering suite - Tutorials · soedinglab/MMseqs2 Wiki

Open Graph Description: MMseqs2: ultra fast and sensitive search and clustering suite - soedinglab/MMseqs2

X Description: MMseqs2: ultra fast and sensitive search and clustering suite - soedinglab/MMseqs2

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	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#table-of-contents
Introduction	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#introduction
Metagenomic pathogen detection	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#metagenomic-pathogen-detection
Contig taxonomic assignment and auxiliary modules	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#contig-taxonomic-assignment-and-auxiliary-modules
Writing large scale sequence analysis workflows	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#writing-large-scale-sequence-analysis-workflows
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#introduction
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#required-software-for-the-tutorials
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https://search.mmseqs.com	https://search.mmseqs.com
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	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#download-swissprot-and-its-associated-taxonomic-information
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	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#analysis-of-a-human-gut-metagenomics-dataset
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	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#learn-how-to-filter-databases
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#what-is-the-difference-to-standard-annotation-tools
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#build-your-own-workflows
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#cascaded-profile-clustering-deep-clustering
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	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#deeper-clustering-using-profiles
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#abundance-analysis
	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#re-create-the-linclust-workflow
real Linclust workflow	https://github.com/soedinglab/MMseqs2/blob/master/data/linclust.sh
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MMseqs2 Developer Guide	https://github.com/soedinglab/MMseqs2/wiki/MMseqs2-Developer-Guide
Please reload this page	https://github.com/soedinglab/MMseqs2/wiki/Tutorials
Tutorials	https://github.com/soedinglab/MMseqs2/wiki/Tutorials
Table of Contents	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#table-of-contents
Introduction	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#introduction
Required software for the tutorials	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#required-software-for-the-tutorials
Metagenomic pathogen detection	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#metagenomic-pathogen-detection
The Patient	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#the-patient
The Dataset	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#the-dataset
Metagenomic pathogen detection using MMseqs2	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#metagenomic-pathogen-detection-using-mmseqs2
Assigning taxonomic labels	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#assigning-taxonomic-labels
Visualizing taxonomic results	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#visualizing-taxonomic-results
What is the pathogen?	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#what-is-the-pathogen
Investigating the pathogen	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#investigating-the-pathogen
Assembling reads to proteins	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#assembling-reads-to-proteins
Clustering to find representative proteins	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#clustering-to-find-representative-proteins
Annotating the proteins	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#annotating-the-proteins
Aftermath	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#aftermath
References	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#references
Contig taxonomic assignment and auxiliary modules	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#contig-taxonomic-assignment-and-auxiliary-modules
Download SwissProt and its associated taxonomic information	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#download-swissprot-and-its-associated-taxonomic-information
Run the MMseqs2 taxonomy	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#run-the-mmseqs2-taxonomy
Produce a TSV report	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#produce-a-tsv-report
Produce a Krona/Kraken visualization	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#produce-a-kronakraken-visualization
Learn more...	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#learn-more
Writing large scale sequence analysis workflows	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#writing-large-scale-sequence-analysis-workflows
Analysis of a human gut metagenomics dataset	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#analysis-of-a-human-gut-metagenomics-dataset
Getting a protein catalogue of a metagenome	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#getting-a-protein-catalogue-of-a-metagenome
Redundancy reduction	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#redundancy-reduction
Learn how to deal with MMseqs2's indexed databases	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#learn-how-to-deal-with-mmseqs2s-indexed-databases
Annotating the catalogue	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#annotating-the-catalogue
Learn how to filter databases	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#learn-how-to-filter-databases
What is the difference to standard annotation tools?	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#what-is-the-difference-to-standard-annotation-tools
Build your own workflows	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#build-your-own-workflows
Cascaded profile clustering (deep clustering)	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#cascaded-profile-clustering-deep-clustering
Cascaded sequence clustering	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#cascaded-sequence-clustering
Deeper clustering using profiles	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#deeper-clustering-using-profiles
Abundance analysis	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#abundance-analysis
Re-create the linclust workflow...	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#re-create-the-linclust-workflow
Conclusion	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#conclusion
References	https://github.com/soedinglab/MMseqs2/wiki/Tutorials#references-1
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