dib-lab's Repositories

Lab information

⭐ 0 🌐 Public

2012-assembly-artifacts

⭐ 0 🌐 Public

2012-assembly-methods

⭐ 2 🌐 Public

2012-paper-diginorm

Paper source, analysis notebook, and data generation/analysis scripts for diginorm paper

⭐ 8 🌐 Public

2012-paper-kmer-percolation

⭐ 4 🌐 Public

2012-posa-chapter

Contributed Chapter for POSA Book

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2013-caltech-workshop

⭐ 3 🌐 Public

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"

⭐ 10 🌐 Public

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2013-msu-zero-entry

A short bootcamp for MSU: zero-entry computational science.

⭐ 1 🌐 Public

2013-paper-outline-index

⭐ 0 🌐 Public

2013-paper-ssspe

4 pager for http://wssspe.researchcomputing.org.uk/

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2013-read-aligner

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2013-reproducible-bioinfo

⭐ 0 🌐 Public

2013-srop-summer

⭐ 2 🌐 Public

2014-elijahlowe-thesis

⭐ 0 🌐 Public

2014-molgula-genome-assemblies

⭐ 0 🌐 Public

2014-mrnaseq-cloud

⭐ 1 🌐 Public

2014-mrnaseq-models

⭐ 0 🌐 Public

2014-paper-cloud-benchmarking

⭐ 0 🌐 Public

2014-paper-wssspe14

⭐ 8 🌐 Public

2014-ssu-search

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⭐ 2 🌐 Public

2015-07-06-ucdavis

⭐ 0 🌐 Public

2015-09-10-scihack

Inaugural Group Science Coding Session

⭐ 2 🌐 Public

2015-khmer-wok1-ec

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2015-khmer-wok2-vc

⭐ 2 🌐 Public

2015-khmer-wok3-counting

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2015-khmer-wok4-multimap

⭐ 1 🌐 Public

2015-khmer-wok5-eval

⭐ 0 🌐 Public

2015-metagenome-assembly

⭐ 2 🌐 Public

2015-paper-10-simple-rules-releasing

⭐ 4 🌐 Public

Many-sample de novo assembly of the sea lamprey transcriptome

⭐ 0 🌐 Public

2016-binder-proposal-to-sloan

⭐ 2 🌐 Public

2016-illo-screed

⭐ 2 🌐 Public

2016-illo-sourmash

⭐ 0 🌐 Public

2016-metagenome-assembly-eval

⭐ 2 🌐 Public

2016-paper-briefings-bioinfo-dc-sc

⭐ 0 🌐 Public

2016-paper-p_asteroides

⭐ 1 🌐 Public

2016-pycon-tutorial

Materials for "Creating, building, testing, and documenting a Python project - a hands-on HOWTO - PyCon 2016"

⭐ 17 🌐 Public

2016-pycon-tutorial-project

⭐ 5 🌐 Public

2016-sourmash-abundstuff

⭐ 0 🌐 Public

2016-sourmash-protstuff

⭐ 0 🌐 Public

2016-sourmash-tax

Taxonomic breakdown of metagenomes using sourmash.

⭐ 2 🌐 Public

2017-06-19-DIBSI-TTT

⭐ 0 🌐 Public

2017-07-05-UCSC

⭐ 0 🌐 Public

2017-dibsi-metagenomics

Workshop materials for shotgun metagenomics

⭐ 0 🌐 Public

2017-ectocooler

⭐ 0 🌐 Public

2017-hdn-explore

⭐ 0 🌐 Public

2017-ncbi-taxdump

⭐ 2 🌐 Public

2017-paper-gather

⭐ 1 🌐 Public

⭐ 3 🌐 Public

2018-06-27-DIBSI-Genomics

DIBSI Data Carpentry Genomics

⭐ 2 🌐 Public

2018-06-27-DIBSI-Geospatial

⭐ 0 🌐 Public

2018-06-27-DIBSI-SocialSci

⭐ 0 🌐 Public

2018-06-27-DIBSI-SWC

⭐ 0 🌐 Public

2018-06-27-SpanishSWC

Website for the Spanish Software Carpentry Workshop at DIBSI

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build sigs and sbt from euk samples

⭐ 0 🌐 Public

2018-mcintyre-output

⭐ 1 🌐 Public

2018-ncbi-lineages

Extract lineage CSVs from NCBI for use with sourmash lca.

⭐ 29 🌐 Public

2018-paper-reanalysis-op-ed

⭐ 1 🌐 Public

2019-12-12-sourmash_viz

⭐ 1 🌐 Public

2019-nih-hgrc-grant

Our application to be the NIH Human Genome Reference Center.

⭐ 2 🌐 Public

2019-oct-speeding-up-science

⭐ 0 🌐 Public

2019-paper-sourmash-f1000

⭐ 0 🌐 Public

2019-sourmash-gtdb

Tools and scripts for studying the GTDB taxonomy with sourmash

⭐ 2 🌐 Public

2020-ggg-201b-lab-hw1

⭐ 0 🌐 Public

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

⭐ 4 🌐 Public

⭐ 1 🌐 Public

2020-paper-mqf-benchmarks

⭐ 1 🌐 Public

2020-paper-sourmash-gather

Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.

⭐ 8 🌐 Public

2020-workflows-paper

Strategies for leveraging workflow systems to streamline large-scale biological analyses

⭐ 6 🌐 Public

2021-metapangenome-example

⭐ 3 🌐 Public

2021-orpheum-sim

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

⭐ 2 🌐 Public

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

⭐ 5 🌐 Public

Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn’s disease

⭐ 5 🌐 Public

2021-paper-metapangenomes

⭐ 1 🌐 Public

2021-paper-sourmash-gather-pipeline

Data analysis pipeline for https://github.com/dib-lab/2020-paper-sourmash-gather/

⭐ 0 🌐 Public

2022-branchwater-benchmarking

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

⭐ 2 🌐 Public

2022-database-covers

⭐ 1 🌐 Public

2022-dominating-set-differential-abundance-example

A reproducible example demonstrating an example workflow for performing dominating set differential abundance analysis

⭐ 2 🌐 Public

2022-donut-ibd-classified-sra-search

⭐ 1 🌐 Public

2022-import-ranger-hashes

Convert ranger random forest models into sourmash signatures

⭐ 1 🌐 Public

2022-paper-branchwater-software

Branchwater (MAGsearch) software paper / manubot

⭐ 0 🌐 Public

2022-paper-genomic-tax-redundancy

Paper: Comprehensive evaluation of genomic redundancy and taxonomic coherence in large biological databases

⭐ 3 🌐 Public

2022-pipeline-antarctic-biogeography

⭐ 1 🌐 Public

2022-read-subtract

Scripts for comparing/subtracting read sets

⭐ 0 🌐 Public

2022-sra-gather

Classify all the metagenomes. ALL THE METAGENOMES. (Eventually.)

⭐ 0 🌐 Public

2023-april-pig-paradigm-meeting

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

⭐ 0 🌐 Public

2023-clean-gtdb

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

⭐ 0 🌐 Public

2024-december-hackathon

Organizing repo for 2024 december hackathon (look at issues)

⭐ 0 🌐 Public

2025-cami-old-db

Process old CAMI II files into sourmash manysketch & lineage formats

⭐ 0 🌐 Public

2025-workflow-core99

Workflow for pig core99 microbiome

⭐ 0 🌐 Public

assembly-exercise

Shotgun sequencing of text, in CGI script form

⭐ 7 🌐 Public

AUGUSTUS v3.2.1 for installation on Mac OS X

⭐ 0 🌐 Public

bioinf_algorithms

Repository for reading group to keep track of work in Bioinformatics Algorithms: an active learning approach

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A project that will change everything. Or something. Or maybe nothing at all.

⭐ 7 🌐 Public