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. 2019 Jul 4:8:1006.
doi: 10.12688/f1000research.19675.1. eCollection 2019.

Large-scale sequence comparisons with sourmash

N Tessa Pierce #  1 , Luiz Irber #  1 , Taylor Reiter #  1 , Phillip Brooks #  1 , C Titus Brown  1
Affiliations

Large-scale sequence comparisons with sourmash

N Tessa Pierce et al. F1000Res. .

Abstract

The sourmash software package uses MinHash-based sketching to create "signatures", compressed representations of DNA, RNA, and protein sequences, that can be stored, searched, explored, and taxonomically annotated. sourmash signatures can be used to estimate sequence similarity between very large data sets quickly and in low memory, and can be used to search large databases of genomes for matches to query genomes and metagenomes. sourmash is implemented in C++, Rust, and Python, and is freely available under the BSD license at http://github.com/dib-lab/sourmash.

Keywords: MinHash; bioinformatics; k-mer; sequence analysis; sourmash.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. The MDS plots produced from the reference-free sourmash compare similarity matrix and the transcript quantification analysis (salmon and edgeR) are similar.
Wild-type S. cerevisiae samples (ERR459011, ERR459102) are in yellow and mutant samples (ERR458584, ERR458829) in blue.
Figure 2.
Figure 2.. Heatmap and dendrogram generated using sourmash signatures built from scaffolds in the domesticated olive genome.
Two scaffolds are outliers when using tetranucleotide frequency to calculate similarity (highlighted in green on the dendrogram).
Figure 3.
Figure 3.. Heatmap and dendrogram generated using sourmash signatures built from 50 genomes that contained the word “ Escherichia coli”.
One signature is an outlier (highlighted in blue on the dendrogram).
See this image and copyright information in PMC

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