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khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and moredammit
just annotate it, dammit!screed
a simple read-only sequence database, designed for short readscharcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.genome-grist
map Illumina metagenomes to genomes!elvers
(formerly eelpond) an automated RNA-Seq workflow system2018-ncbi-lineages
Extract lineage CSVs from NCBI for use with sourmash lca.dib-MMETSP
Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)khmer-protocols
pybbhash
A Python wrapper for the bbhash library for Minimal Perfect Hashing2016-pycon-tutorial
Materials for "Creating, building, testing, and documenting a Python project - a hands-on HOWTO - PyCon 2016"farm-notes
notes on the farm clusterMQF
kProcessor
kProcessor: kmers processing framework.literate-resting
Scripts and code for development of literate testing with reST-based shell tutorials.kmerDecoder
Extract kmers, skipmers, minimizers.2013-khmer-counting
Paper code: "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure"rcgrep
Search text files for DNA sequences and their reverse complementskhmer-recipes
kSpider
A simple yet powerful sequence clustering tool.dib-training
Web site for Data Intensive Training at UC Davis2020-paper-sourmash-gather
Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.TransAnn-Review
buoy
A project that will change everything. Or something. Or maybe nothing at all.syrah
Output trusted regions from raw sequencing data.2020-workflows-paper
Strategies for leveraging workflow systems to streamline large-scale biological analysesdib-lab
Issue tracker and Web site for the Lab for Data Intensive Biology at UC Davis.workflows-book
Issues and draft text for "The Workflow Enabled Bioinformatician"2014-paper-wssspe14
2016-pycon-tutorial-project
distillerycats
Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.2021-panmers
Exploring amino acid kmers as a substitute for genes in microbial pangenome analysis2020-ibd
Analysis of publicly available metagenomic sequencing data from humans with IBD.2015-paper-10-simple-rules-releasing
q2-sourmash
Qiime2 Sourmash Plugin2021-paper-ibd
Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease2012-paper-kmer-percolation
bioinf_algorithms
Repository for reading group to keep track of work in Bioinformatics Algorithms: an active learning approach2013-caltech-workshop
dibsi
Data Intensive Biology Summer Institute2017-tule-elk
2021-metapangenome-example
sourmash-oddify
Tools and workflows for evaluating bacterial and archaeal genome contamination with sourmash and GTDB.2022-paper-genomic-tax-redundancy
Paper: Comprehensive evaluation of genomic redundancy and taxonomic coherence in large biological databasesdib_rotation
Metagenomics DIB-lab rotation projectTheGreatGenotyper
workshop_12Jan_2023
2019-nih-hgrc-grant
Our application to be the NIH Human Genome Reference Center.2016-illo-screed
khmer-batlab
batlab.org build scripts2012-assembly-methods
ONT_Illumina_genome_assembly
Genome assemblies of Fundulus killifish species with ONT and Illumina sequence data2021-orpheum-sim
Simulate short sequencing reads from coding and non-coding portions of bacterial and archaeal genomes to evaluate orpheum ORF prediction2016-binder-proposal-to-sloan
2022-branchwater-benchmarking
Benchmarking etc code for https://dib-lab.github.io/2022-paper-branchwater-software/CarpentryConWest18
The GitHub repo for CarpentryConnect Davis (formerly known as CarpentryConWest)2016-sourmash-tax
Taxonomic breakdown of metagenomes using sourmash.2017-ncbi-taxdump
2013-srop-summer
soursigs
2015-09-10-scihack
Inaugural Group Science Coding Session2019-sourmash-gtdb
Tools and scripts for studying the GTDB taxonomy with sourmash2018-06-27-DIBSI-Genomics
DIBSI Data Carpentry Genomicseel-pond
mRNAseq assembly, evaluation, and expression analysis2016-metagenome-assembly-eval
2022-dominating-set-differential-abundance-example
A reproducible example demonstrating an example workflow for performing dominating set differential abundance analysis2018-mcintyre-output
oxli
k-mers and the likesourmash-slainte
Project template for sourmash-based characterization of genomes and metagenomes2022-pipeline-antarctic-biogeography
khmer-citation
The paper that is the citation handle for khmer software.2021-paper-metapangenomes
Haemonchus-pipeline
Automated pipeline to process genomic and RNASeq reads from Haemonchus contortus into a draft genome assembly and draft transcriptomic assembly.2018-paper-reanalysis-op-ed
portable-snakemake-workflows
A small, fast, robust workflows using snakemake!2020-NSURP
mkdocs-material-dib
Mkdocs theme for documentation for DIB Lab software.2013-msu-zero-entry
A short bootcamp for MSU: zero-entry computational science.2022-donut-ibd-classified-sra-search
2022-database-covers
2020-paper-mqf-benchmarks
2017-paper-gather
training-by-practice
sourmash-utils
Scripts that are useful for sourmash, but not necessarily part of the base command line.2014-mrnaseq-cloud
sourmash_plugin_pangenomics
tools for sourmash-based pangenome analyses2022-import-ranger-hashes
Convert ranger random forest models into sourmash signatures2019-12-12-sourmash_viz
sourmash_plugin_colorcompare
Add colors representing categories in sourmash compare plots.Love Open Source and this site? Check out how you can help us