The Lab for Data Intensive Biology

The Lab for Data Intensive Biology at UC Davis

In addition to the pinned repositories within dib-lab, we also work on and help maintain the following software:

sourmash, for rapid large-scale sequence search.

spacegraphcats, for querying large annoying metagenome assembly graphs.

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

Python 786 298
Remove contaminated contigs from genomes using k-mers and taxonomies.

Python 60 2
map Illumina metagenomes to genomes!

Jupyter Notebook 38 6

Showing 10 of 177 repositories

dib-lab/2025-workflow-core99’s past year of commit activity

Jupyter Notebook 0 BSD-3-Clause 0
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screed Public
a simple read-only sequence database, designed for short reads

dib-lab/screed’s past year of commit activity

Python
65 32 10 4
Updated Feb 16, 2026
dib-lab/q2-sourmash’s past year of commit activity

Python
6
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Updated Jan 27, 2026
dib-lab/genome-grist’s past year of commit activity
dib-lab/sourmash_plugin_pangenomics’s past year of commit activity

Python
1
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1 6 3
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dib-lab/sourmash-midgie-raker’s past year of commit activity

Jupyter Notebook
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pybbhash Public
A Python wrapper for the bbhash library for Minimal Perfect Hashing

dib-lab/pybbhash’s past year of commit activity

C++
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Updated Oct 26, 2025
kmerDecoder Public
Extract kmers, skipmers, minimizers.

dib-lab/kmerDecoder’s past year of commit activity

C++
10 3 15 0
Updated Oct 24, 2025
dib-lab Public
Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.

dib-lab/dib-lab’s past year of commit activity

Python
8 20 44 2
Updated Oct 13, 2025
dib-lab/2022-branchwater-benchmarking’s past year of commit activity

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Updated Sep 17, 2025