GTDB databases!
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Comparing two genome binnings quickly with sourmash
Things to think about when developing shotgun metagenome classifiers
Detecting microbial contamination in long-read assemblies (from known microbes)
Advancing metagenome classification and comparison by MinHash fingerprinting of IMG/M data sets.
This is our just-submitted proposal for the JGI-NERSC "Facilities Integrating Collaborations for User Science" call. Enjoy!
- Brief description: (Limit 1 page)
Abstract: Sourmash is a command-line tool and Python library that calculates and compares MinHash signatures from sequence data. Sourmash "compare" and "gather" functionality enables comparison and characterization of signatures …
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Categorizing 400,000 microbial genome shotgun data sets from the SRA
This is another blog post on MinHash sketches; see also:
- Applying MinHash to cluster RNAseq samples
- MinHash signatures as ways to find samples, and collaborators?
- Efficiently searching MinHash Sketch collections
- Quickly searching all the microbial genomes, mark 2 - now with archaea, phage, fungi, and protists!
- What metadata should we put …
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What metadata should we put in MinHash Sketch signatures?
One of the uses that we are most interested in MinHash sketches for is the indexing and search of large public, semi-public, and private databases. There are many specific use cases for this, but the basic goal is to be able to find data sets by content queries, using sequence …
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