brooksph

2017_Hum_and_murine_microbiota_mouse_analysis

2017_sourmash_gather_comparison

comparing sourmash gather functionality to other tools with similar capabilities

2017-cicese-metagenomics

2017-dibsi-metagenomics

Workshop materials for shotgun metagenomics

2017-dibsi-rnaseq

2017_Dysfunction_of_the_gut_microbiome

2017_Humanized_micrbiota_16S_comparison

2017_sbt_search_project

2017_sourGUT

2017_viral_genome_association_study

Extracting viral genomes from shotgun metagenomes using sourmash

2020-workflows-paper

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

abstracts

Abstracts for meetings

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bioconda-recipes

Conda recipes for the bioconda channel.

brooksph.github.io

Personal website

dahak

benchmarking and containerization of tools for analysis of complex non-clinical metagenomes

Dahak_examples

Example notebooks for end user data exploration

dahak_notes

Notes for Dahak project

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Kraken_db_install_scripts

Updated Kraken DB install scripts to cope with new-ish NCBI structure

organization-genomics

PR2017replicaton

py-upset

A pure-python implementation of the UpSet suite of visualisation methods by Lex, Gehlenborg et al.

reference_genome_exploration

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

shell-novice

Software Carpentry introduction to the shell for novices.

shotmap

A Shotgun Metagenome Annotation Pipeline

tara-sourmash

UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..