The Lab for Data Intensive Biology

Previously "Genomics, Evolution, and Development Lab" @ Michigan State University

University of California, Davis, School of Veterinary Medicine, Davis, California, USA
http://ivory.idyll.org/lab/

2020-paper-sourmash-gather Public
Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.

HTML 4 1 23 1 Updated Dec 2, 2021
kProcessor Public
kProcessor: kmers processing framework.

C++ 7 BSD-3-Clause 1 50 (4 issues need help) 5 Updated Nov 26, 2021
farm-notes Public
notes on the farm cluster

12 6 11 2 Updated Nov 24, 2021
2020-ibd Public
Analysis of publicly available metagenomic sequencing data from humans with IBD.

R 3 0 6 0 Updated Nov 23, 2021
kSpider Public
A simple yet powerful sequence clustering tool.

Python 0 MIT 1 1 1 Updated Nov 23, 2021
kmerDecoder Public
Extract kmers, skipmers, minimizers.

C++ 8 3 12 1 Updated Nov 20, 2021
2021-paper-sourmash-gather-pipeline Public
Data analysis pipeline for https://github.com/dib-lab/2020-paper-sourmash-gather/

Jupyter Notebook 0 BSD-3-Clause 0 0 1 Updated Nov 4, 2021
genome-grist Public
map Illumina metagenomes to GenBank genomes

Jupyter Notebook 13 3 52 3 Updated Nov 3, 2021
charcoal Public
Remove contaminated contigs from genomes using k-mers and taxonomies.

Standard ML 19 1 94 4 Updated Nov 1, 2021
dib-lab Public
Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.

Python 5 18 43 2 Updated Oct 4, 2021

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