The Lab for Data Intensive Biology

khmer

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

dammit

just annotate it, dammit!

screed

a simple read-only sequence database, designed for short reads

charcoal

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

genome-grist

map Illumina metagenomes to genomes!

2018-ncbi-lineages

Extract lineage CSVs from NCBI for use with sourmash lca.

pybbhash

A Python wrapper for the bbhash library for Minimal Perfect Hashing

farm-notes

notes on the farm cluster

MQF

kProcessor

kProcessor: kmers processing framework.

kSpider

A simple yet powerful sequence clustering tool.

dib-lab

Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.

2021-panmers

Exploring amino acid kmers as a substitute for genes in microbial pangenome analysis

2020-ibd

Analysis of publicly available metagenomic sequencing data from humans with IBD.

q2-sourmash

Qiime2 Sourmash Plugin

2021-metapangenome-example

2021-orpheum-sim

Simulate short sequencing reads from coding and non-coding portions of bacterial and archaeal genomes to evaluate orpheum ORF prediction

2022-branchwater-benchmarking

Benchmarking etc code for https://dib-lab.github.io/2022-paper-branchwater-software/

dib_rotation

Metagenomics DIB-lab rotation project

workshop_12Jan_2023

2021-paper-metapangenomes

2022-database-covers

portable-snakemake-workflows

A small, fast, robust workflows using snakemake!

sourmash_plugin_colorcompare

Add colors representing categories in sourmash compare plots.

2023-clean-gtdb

An experimental snakemake workflow repository to remove suppressed or replaced genomes from sourmash workflows

2023-april-pig-paradigm-meeting

PIG-PARADIGM meeting at UC Davis, April 18 and 19th, 2023.

Cattle_Structural_Variant_Benchmark

Cattle_SV_Catalog

sourmash-slainte

Project template for sourmash-based characterization of genomes and metagenomes

TheGreatGenotyper