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
Pinned Repositories
2018-ncbi-lineages
Extract lineage CSVs from NCBI for use with sourmash lca.
charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
dammit
just annotate it, dammit!
dib-MMETSP
Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)
elvers
(formerly eelpond) an automated RNA-Seq workflow system
genome-grist
map Illumina metagenomes to genomes!
khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
khmer-protocols
pybbhash
A Python wrapper for the bbhash library for Minimal Perfect Hashing
screed
a simple read-only sequence database, designed for short reads
The Lab for Data Intensive Biology's Repositories
dib-lab/elvers
(formerly eelpond) an automated RNA-Seq workflow system
dib-lab/2020-paper-sourmash-gather
Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.
dib-lab/dib-training
Web site for Data Intensive Training at UC Davis
dib-lab/2020-workflows-paper
Strategies for leveraging workflow systems to streamline large-scale biological analyses
dib-lab/2021-panmers
Exploring amino acid kmers as a substitute for genes in microbial pangenome analysis
dib-lab/2021-paper-ibd
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease
dib-lab/distillerycats
Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.
dib-lab/2020-ibd
Analysis of publicly available metagenomic sequencing data from humans with IBD.
dib-lab/2021-metapangenome-example
dib-lab/2022-paper-genomic-tax-redundancy
Paper: Comprehensive evaluation of genomic redundancy and taxonomic coherence in large biological databases
dib-lab/dibsi
Data Intensive Biology Summer Institute
dib-lab/sourmash-oddify
Tools and workflows for evaluating bacterial and archaeal genome contamination with sourmash and GTDB.
dib-lab/2021-orpheum-sim
Simulate short sequencing reads from coding and non-coding portions of bacterial and archaeal genomes to evaluate orpheum ORF prediction
dib-lab/2022-dominating-set-differential-abundance-example
A reproducible example demonstrating an example workflow for performing dominating set differential abundance analysis
dib-lab/ONT_Illumina_genome_assembly
Genome assemblies of Fundulus killifish species with ONT and Illumina sequence data
dib-lab/workshop_12Jan_2023
dib-lab/2019-12-12-sourmash_viz
dib-lab/2020-paper-mqf-benchmarks
dib-lab/2022-donut-ibd-classified-sra-search
dib-lab/2022-import-ranger-hashes
Convert ranger random forest models into sourmash signatures
dib-lab/2022-pipeline-antarctic-biogeography
dib-lab/.github
Lab information
dib-lab/2021-paper-sourmash-gather-pipeline
Data analysis pipeline for https://github.com/dib-lab/2020-paper-sourmash-gather/
dib-lab/2022-paper-branchwater-software
Branchwater (MAGsearch) software paper / manubot
dib-lab/2022-read-subtract
Scripts for comparing/subtracting read sets
dib-lab/2022-sra-gather
Classify all the metagenomes. ALL THE METAGENOMES. (Eventually.)
dib-lab/2023-april-pig-paradigm-meeting
PIG-PARADIGM meeting at UC Davis, April 18 and 19th, 2023.
dib-lab/kProcessor_tests
Testing kProcessor framework
dib-lab/kProcessor_wheels
dib-lab/ribbity-workshops
a repo for making workshops from github issues