Additional information on sourmash¶
Computational requirements¶
Read more about the computational requirements, here.
Prepared search databases¶
We offer a number of prepared search databases.
You can read about the supported database formats here.
Other MinHash implementations for DNA¶
In addition to mash, also see:
RKMH: Read Classification by Kmers
mashtree: For building trees using Mash
Finch: “Fast sketches, count histograms, better filtering.”
BBMap and SendSketch: part of Brian Bushnell’s tool collection.
PATRIC uses MinHash for genome search.
If you are interested in exactly how these MinHash approaches calculate the hashes of DNA sequences, please see some simple Python code in sourmash, utils/compute-dna-mh-another-way.py
Papers and references¶
On the resemblance and containment of documents, Broder, 1997. The original MinHash paper!
Mash: fast genome and metagenome distance estimation using MinHash., Ondov et al. 2016.
sourmash: a library for MinHash sketching of DNA., Brown and Irber, 2017.
Improving MinHash via the Containment Index with Applications to Metagenomic Analysis, Koslicki and Zabeti, 2017.
Ultra-fast search of all deposited bacterial and viral genomic data, Bradley et al., 2019.
Streaming histogram sketching for rapid microbiome analytics, Rowe et al., 2019.
Dashing: Fast and Accurate Genomic Distances with HyperLogLog, Baker and Langmead, 2019.
Presentations and posters¶
Taxonomic classification of microbial metagenomes using MinHash signatures, Brooks et al., 2017. Presented at ASM.
Blog posts¶
We (and others) have a number of blog posts on sourmash and MinHash more generally:
From the Phillippy lab: mash screen: what’s in my sequencing run?
MinHash signatures as ways to find samples, and collaborators?
Efficiently searching MinHash Sketch collections: indexing and search 42,000 bacterial genomes with Sequence Bloom Trees.
Quickly searching all the microbial genomes, mark 2 - now with archaea, phage, fungi, and protists!: indexing and searching 50,000 microbial genomes, round 2.
What metadata should we put in MinHash Sketch signatures?: crowdsourcing ideas for what metadata belongs in a signature file.
Minhashing all the things (part 1): microbial genomes: on approaches to computing MinHashes for large collections of public data.
Classifying genome bins using a custom reference database, part I
Classifying genome bins using a custom reference database, part II
JSON format for the signature¶
The JSON format is not necessarily final; this is a TODO item for future releases. In particular, we’d like to update it to store more metadata for samples.
Interoperability with mash¶
The hashing functions used by sourmash and mash are the same, but we
are still working on ways to convert the file formats. Please
keep an eye on sourmash signature import and sourmash signature export!
Developing sourmash¶
Please see:
Known issues¶
For at least some versions of matplotlib, users may encounter an error “Failed to connect to server socket:” or “RuntimeError: Invalid DISPLAY variable”. This is because by default matplotlib tries to connect to X11 to use the Tkinter backend.
The solution is to force the use of the ‘Agg’ backend in matplotlib; see this stackoverflow answer or this sourmash issue comment.
Newer versions of matplotlib do not seem to have this problem.
