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.
Language:Python27 4 06
charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
Language:Python53 19 1631
dammit
just annotate it, dammit!
Language:Python89 13 16528
dib-MMETSP
Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)
Language:Python21 8 36
elvers
(formerly eelpond) an automated RNA-Seq workflow system
Language:Python28 6 993
genome-grist
map Illumina metagenomes to genomes!
Language:Jupyter Notebook37 22 1716
khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Language:Python757 68 1k295
khmer-protocols
Language:Python19 29 7724
pybbhash
A Python wrapper for the bbhash library for Minimal Perfect Hashing
Language:C++18 6 114
screed
a simple read-only sequence database, designed for short reads
Language:Python63 25 1134

The Lab for Data Intensive Biology's Repositories

dib-lab/khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
Language:Python757 68 1k295
dib-lab/dammit
just annotate it, dammit!
Language:Python89 13 16528
dib-lab/screed
a simple read-only sequence database, designed for short reads
Language:Python63 25 1134
dib-lab/charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
Language:Python53 19 1631
dib-lab/genome-grist
map Illumina metagenomes to genomes!
Language:Jupyter Notebook37 22 1716
dib-lab/2018-ncbi-lineages
Extract lineage CSVs from NCBI for use with sourmash lca.
Language:Python27 4 06
dib-lab/pybbhash
A Python wrapper for the bbhash library for Minimal Perfect Hashing
Language:C++18 6 114
dib-lab/farm-notes
notes on the farm cluster
16 13 479
dib-lab/MQF
Language:C++12 6 70
dib-lab/kProcessor
kProcessor: kmers processing framework.
Language:C++11 6 801
dib-lab/kmerDecoder
Extract kmers, skipmers, minimizers.
Language:C++10 5 323
dib-lab/kSpider
A simple yet powerful sequence clustering tool.
Language:C++8 5 241
dib-lab/assembly-exercise
Shotgun sequencing of text, in CGI script form
Language:Python7 4 06
dib-lab/dib-lab
Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.
Language:Python7 26 7519
dib-lab/q2-sourmash
Qiime2 Sourmash Plugin
Language:Python4 7 34
dib-lab/dib_rotation
Metagenomics DIB-lab rotation project
Language:Python3 18 518
dib-lab/TheGreatGenotyper
Language:C++3 8 10
dib-lab/2022-branchwater-benchmarking
Benchmarking etc code for https://dib-lab.github.io/2022-paper-branchwater-software/
Language:Jupyter Notebook2 3 5
dib-lab/2020-NSURP
Language:Python1 22 10
dib-lab/2021-paper-metapangenomes
Language:HTML1 3 102
dib-lab/2022-database-covers
Language:Python1 2 62
dib-lab/portable-snakemake-workflows
A small, fast, robust workflows using snakemake!
Language:Python1 9 51
dib-lab/sourmash-slainte
Project template for sourmash-based characterization of genomes and metagenomes
Language:Python1 3 7
dib-lab/sourmash_plugin_colorcompare
Add colors representing categories in sourmash compare plots.
Language:Python1 3 0
dib-lab/sourmash_plugin_pangenomics
tools for sourmash-based pangenome analyses
Language:Python1 2 5
dib-lab/2023-clean-gtdb
An experimental snakemake workflow repository to remove suppressed or replaced genomes from sourmash workflows
Language:Python0 3 10
dib-lab/Cattle_Structural_Variant_Benchmark
Language:Python3 0
dib-lab/Cattle_SV_Catalog
3 0
dib-lab/TheGreatGenotyper_benchmark
Language:Python2 0
dib-lab/TheGreatGenotyper_usecases
Language:Python2 0