Discover dib-lab/2022-pipeline-antarctic-biogeography Open Source

just annotate it, dammit!

749

dammit

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

screed

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

charcoal

map Illumina metagenomes to genomes!

genome-grist

(formerly eelpond) an automated RNA-Seq workflow system

elvers

Extract lineage CSVs from NCBI for use with sourmash lca.

2018-ncbi-lineages

Code to generate re-assemblies of the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP)

dib-MMETSP

khmer-protocols

A Python wrapper for the bbhash library for Minimal Perfect Hashing

pybbhash

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

2016-pycon-tutorial

farm-notes

notes on the farm cluster

MQF

kProcessor: kmers processing framework.

kProcessor

Scripts and code for development of literate testing with reST-based shell tutorials.

literate-resting

Extract kmers, skipmers, minimizers.

kmerDecoder

Paper code: "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure"

2013-khmer-counting

Search text files for DNA sequences and their reverse complements

rcgrep

khmer-recipes

A simple yet powerful sequence clustering tool.

kSpider

Web site for Data Intensive Training at UC Davis

dib-training

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

2020-paper-sourmash-gather

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

TransAnn-Review

buoy

syrah

Output trusted regions from raw sequencing data.

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

2020-workflows-paper

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

dib-lab

Issues and draft text for "The Workflow Enabled Bioinformatician"

workflows-book

2014-paper-wssspe14

2016-pycon-tutorial-project

Holding repository for GED internal documentation of commonly-used tools, with a focus on power-users.

ged-docs

Find disease associations across metagenomes with k-mers using sourmash, and then recover pangenomic accessory elements using spacegraphcats.

distillerycats

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

2021-panmers

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

2020-ibd

2015-paper-10-simple-rules-releasing

q2-sourmash

Qiime2 Sourmash Plugin

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

2021-paper-ibd

2012-paper-kmer-percolation

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

bioinf_algorithms

2013-caltech-workshop

Data Intensive Biology Summer Institute

dibsi

2017-tule-elk

Shell

2021-metapangenome-example

Tools and workflows for evaluating bacterial and archaeal genome contamination with sourmash and GTDB.

sourmash-oddify

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

2022-paper-genomic-tax-redundancy

Metagenomics DIB-lab rotation project

dib_rotation

TheGreatGenotyper

workshop_12Jan_2023

Our application to be the NIH Human Genome Reference Center.

2019-nih-hgrc-grant

2016-illo-screed

Genome assemblies of Fundulus killifish species with ONT and Illumina sequence data

khmer-batlab

batlab.org build scripts

Shell

2012-assembly-methods

ONT_Illumina_genome_assembly

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

2021-orpheum-sim

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

2016-binder-proposal-to-sloan

2022-branchwater-benchmarking

The GitHub repo for CarpentryConnect Davis (formerly known as CarpentryConWest)

CarpentryConWest18

2016-sourmash-tax

Taxonomic breakdown of metagenomes using sourmash.

2017-ncbi-taxdump

2013-srop-summer

soursigs

Inaugural Group Science Coding Session

2015-09-10-scihack

Tools and scripts for studying the GTDB taxonomy with sourmash

2019-sourmash-gtdb

DIBSI Data Carpentry Genomics

2018-06-27-DIBSI-Genomics

mRNAseq assembly, evaluation, and expression analysis

eel-pond

2016-metagenome-assembly-eval

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

2022-dominating-set-differential-abundance-example

2018-mcintyre-output

Project template for sourmash-based characterization of genomes and metagenomes

oxli

k-mers and the like

Rust

sourmash-slainte

The paper that is the citation handle for khmer software.

khmer-citation

2021-paper-metapangenomes

Automated pipeline to process genomic and RNASeq reads from Haemonchus contortus into a draft genome assembly and draft transcriptomic assembly.

Haemonchus-pipeline

2018-paper-reanalysis-op-ed

A small, fast, robust workflows using snakemake!

portable-snakemake-workflows

2020-NSURP

Mkdocs theme for documentation for DIB Lab software.

mkdocs-material-dib

CSS

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

Scripts that are useful for sourmash, but not necessarily part of the base command line.

training-by-practice

Shell

sourmash-utils

2014-mrnaseq-cloud

tools for sourmash-based pangenome analyses

sourmash_plugin_pangenomics

Convert ranger random forest models into sourmash signatures

2022-import-ranger-hashes

2019-12-12-sourmash_viz

Add colors representing categories in sourmash compare plots.

sourmash_plugin_colorcompare