Shaun Jackman

Login: sjackman

Company: University of British Columbia, BC Cancer Agency Genome Sciences Centre

Location: Vancouver, Canada

Bio: I am a bioinformatics PhD student, a developer of Linuxbrew and ABySS, an open-source programmer, an avid traveller, a singer and an experimental cook.

Blog: http://sjackman.ca

Blog: http://sjackman.ca

Member of

1. BC Cancer Agency Canada's Michael Smith Genome Sciences Centre
2. Brewsci
3. Linuxbrew
4. STAT 545 @ University of British Columbia

Repositories

2013-11_sfu

Supporting documents for talk and workshop for SFU Statistics and Actuarial Science

2013-davis-assembly

null

abstracts

Conference abstracts

abyss

:microscope: Assemble large genomes using short reads

abyss2-slides

ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter

abyss-activity

ABySS learning activity

abyss-drosophila-melanogaster

:microscope: Assemble Drosophila melanogaster with ABySS

abyss-pipeline

Scaling ABySS to longer reads using spaced k-mers and Bloom filters

abyss-scaffold-paper

Scaffolding a genome sequence assembly using ABySS

angus

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

arcs

Scaffold genome sequence assemblies using 10x Genomics data

assembler-components

Components of genome sequence assembly tools

assembly-graph

Compare assembly graph file formats

assembly-slides

Genome sequence assembly slides

awesome-10x-genomics

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

bam-readcount

count DNA sequence reads in BAM files

bamtools

C++ API & command-line toolkit for working with BAM data

barrnap

Bacterial ribosomal RNA predictor

bc

Template for Software Carpentry bootcamp site repository.

bcalm

de Bruijn graph compaction in low memory

beautiful-jekyll

Build a beautiful and simple website in literally minutes. Demo at http://deanattali.com/beautiful-jekyll

bedtools2

A powerful toolset for genome arithmetic.

BEETL

BEETL

bfc

High-performance error correction for Illumina resequencing data

bioawk

BWK awk modified for biological data

bioconda-recipes

Conda recipes for the bioconda channel.

biomake

GNU-Make-like utility for managing builds and complex workflows

biomakefile

Makefile library for bioinformatics programs, with a focus on next-generation sequencing

bosc2015

Content from BOSC2015 unconference sessions on building successful open source bioinformatics communities

bowtie2

A fast and sensitive gapped read aligner

brew

:beer::penguin: The Homebrew package manager for Linux

brew-evolution

:fast_forward: Proposals for changes to the Homebrew package manager.

bwa

Burrow-Wheeler Aligner

bxtools

Tools for analyzing 10X Genomics data

coreos-vagrant

Minimal Vagrantfile for CoreOS

cpsc540-project

CPSC 540 Term Project

DALIGNER

Find all significant local alignments between reads

dbgfm

FM-index representation of a de Bruijn graph

debruijn

de Bruijn graph construction tool

dev-sea-el

command line access to devtools

distance-estimator-paper

Estimate the distance between two nucleotide sequence fragments using paired-end reads

distroless

? Language focused docker images, minus the operating system.

docker

:whale: :penguin: Dockerfiles for running Linuxbrew on various distros

docker-abyss

Docker container for abyss genome assembler

docker-bio

Docker images of bioinformatics software

docker-linuxbrew

:skull: Defunct. Use https://github.com/Linuxbrew/docker

dotfiles

~/.*

drake

Data workflow tool, like a "Make for data"

DWGSIM

Whole Genome Simulator for Next-Generation Sequencing

exonerate

A generic tool for sequence alignment

fastascripts

Manipulate FASTA files

fastgtools

Tools to manipulate FASTG files

galaxytools

:microscope::books: Galaxy Tool wrappers

genometools

GenomeTools genome analysis system.

gfa2-slides

:microscope: Graphical Fragment Assembly (GFA) 2.0

gfalint

Check a GFA file for syntax errors

GFA-spec

Graphical Fragment Assembly (GFA) Format Specification

gff3toembl

Convert a GFF3 file to a format acceptable for submission to EMBL

ggplot2-tutorial

Teaching materials for the R package ggplot2

giab-slides

Assembling the Genome in a Bottle sequencing data with ABySS

gt-userscripts

GenomeTools Lua userscripts.

hackseq_2017_project_6

ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads

happy-git-with-r

Using Git and GitHub with R, Rstudio, and R Markdown

homebrew

? The missing package manager for macOS

homebrew-base

Science formulae for the Linuxbrew and Homebrew package managers

homebrew-bio

:beer::microscope::penguin: Bioinformatics formulae for the Linuxbrew package manager

homebrew-bundle

:package: Bundler for non-Ruby dependencies from Homebrew

homebrew-cask

a friendly homebrew-style CLI workflow for the administration of Mac applications distributed as binaries

homebrew-core

:beers::penguin: Core formulae for the Linuxbrew package manager

homebrew-core-macos

? Default formulae for the missing package manager for macOS

homebrew-desc

Searchable descriptions for Homebrew formulas

homebrew-developer

:wrench::penguin: Tools for Linuxbrew developers

homebrew-dupes

:two_women_holding_hands: System duplicate formulae for the Homebrew package manager

homebrew-extra

:lollipop::penguin: Linux-only formulae that are not dependencies of core formulae

homebrew-php

:earth_americas: PHP formulae repo for Homebrew

homebrew-portable

? Versions of Ruby, Git and Curl that can be installed and run from anywhere on the filesystem.

homebrewr

An R package to install software using Homebrew

homebrew-sandbox

A testing ground for the Brewsci organization

homebrew-science

Scientific formulae for the Homebrew and Linuxbrew package managers

homebrew-science-deprecated

:microscope: Scientific formulae for the Homebrew package manager

homebrew-tap

Personal formulae for the Homebrew package manager

homebrew-test-bot

? Tests the full lifecycle of a Homebrew change.

homebrew-versions

Versioned formulae for the Homebrew package manager

homebrew-x11

Applications with hard X11 dependencies

homebrew-xorg

:heavy_multiplication_x: X.Org implementation of the X Window System

htslib

C library for high-throughput sequencing data formats. This is the official repository.

IGV

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

install

:inbox_tray: A fork of Homebrew's installer for Linuxbrew

Jellyfish

A fast multi-threaded k-mer counter

jmazz.me

null

KAT

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

khmer

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

KmerStream

Streaming algorithm for computing kmer statistics for massive genomics datasets

konnector-vis

Visualize an ABySS-Konnector graph

lambdar

?R: Run R on AWS Lambda

large-molecule-slides

:microscope: Assembling Genomes Using Large Molecule Sequencing

lariat

Linked-Read Alignment Tool

LINKS

Long Interval Nucleotide K-mer Scaffolder

linuxbrew

A fork of Homebrew for Linux

linuxbrew-lambda

Transfer bottles from CircleCI to BinTray and GitHub

linuxbrew-paper

:beer::penguin: Linuxbrew Enables Repeatable Cross-Platform Scientific Software Installation

linuxbrew-slides

Linuxbrew and Homebrew-Science

lobstr-code

lobSTR: a short tandem repeat profiler for next generation sequencing data

makefile2graph

Creates a graph of dependencies from GNU-Make; Output is a graphiz-dot file or a Gexf-XML file.

makefile-example

An example of a data analysis pipeline using Make

makefile-example-stat545

Makefile example for STAT 545

makefile-slides

:microscope: Automating Data Analysis Pipelines

mars-rover

:rocket: Extraterrestrial DNA! :rocket:

mathiasbynens-dotfiles

.files, including ~/.osx ? sensible hacker defaults for OS X

miller

Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

nanocorrect

Experimental pipeline for correcting nanopore reads

nanopolish

Signal-level algorithms for MinION data

nanopore-paper-analysis

Code for nanopore paper

networkx

Official NetworkX source code repository.

ntCard

Estimating k-mer coverage histogram of genomics data

nucleotides-data

Structured input data for

nycflights13

An R data package containing all out-bound flights from NYC in 2013 + useful metdata

ococo

OCOCO: the first online consensus caller. Call genomic consensus directly from a SAM/BAM stream.

OGDraw

A mirror of OrganellarGenomeDRAW

open-science

:microscope: Open, reproducible science using Make, RMarkdown and Pandoc

orca

:whale: Genomics Research Container Architecture

orca-paper

:whale::beer::penguin: ORCA: Genomics Research Container Architecture

peer_review

Validates whether a given email, url, or domain belongs to a research institution.

pgcpdna

:evergreen_tree: Annotate the plastid genome of white spruce (Picea glauca)

pgcpdna-wgs-assembly

:evergreen_tree: Analyze plastid DNA (cpDNA) of white spruce (Picea glauca)

pgmtdna

:evergreen_tree: Annotate the mitochondrial genome of white spruce (Picea glauca)

pg-odna-transfer

:evergreen_tree: Analyze organellar DNA transfer in white spruce (Picea glauca)

picea-glauca-organelles

:evergreen_tree: Align linked reads to the white spruce organelles

picea-sitchensis-mitochondrion

:evergreen_tree: Mitochondrial genome of Sitka spruce (Picea sitchensis)

picea-sitchensis-organelles-poster

:evergreen_tree: Organellar Genomes of Sitka Spruce (Picea sitchensis): Assembly and Annotation

picea-sitchensis-organelles-slides

:evergreen_tree: Organellar Genomes of Sitka Spruce (Picea sitchensis): ?Assembly and Annotation

picea-sitchensis-plastid

:evergreen_tree: Annotate the plastid genome of Sitka spruce (Picea sitchensis)

pigz

A parallel implementation of gzip for modern multi-processor, multi-core machines.

playground

A playground for experimentation

Prodigal

Prodigal Gene Prediction Software

prokka

Rapid prokaryotic genome annotation

psitchensismt

? Mitochondrial genome of Sitka spruce (Picea sitchensis)

purrr

Make your pure R function purrr with functional programming

quast

Genome assembly evaluation tool

readr

Read flat files (csv, tsv, fwf) into R

resume

Shaun Jackman's resume

review-regionReport

Review of regionReport

rewrite-git-history

Rewrite the history of a git fork to match the history of its parent

rocket

App Container runtime

rosalind

Rosalind solutions in Haskell

sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads

salmon

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

samskrit

Tools to manipulate SAM and BAM files

samtools

null

scaffolding-coverage

Determine the required mate-pair coverage for scaffolding

scikit-learn

scikit-learn: machine learning in Python

sga

de novo sequence assembler using string graphs

sickle

Windowed Adaptive Trimming for fastq files using quality

site

Software Carpentry web site.

sjackman.github.io

The personal web site of Shaun Jackman

snoove

Create a dendrogram from genome sequencing data

Spearmint

Spearmint Bayesian optimization codebase

squeakr

Squeakr: An Exact and Approximate k -mer Counting System

sra-tools

SRA Tools

stat540-project

STAT 540 group project

styles

Official repository for Citation Style Language (CSL) citation styles.

tabtools

Scripts to manipulate tab-delimited data

thesis-committee

PhD thesis committee presentation slides

tigerbrew

Experimental fork of homebrew for PPC Macs on Tiger

tigmint-data

Correct misassemblies using Tigmint

tigmint-recomb-slides

Tigmint: Correcting Misassemblies Using Linked Reads From Large Molecules

tigmint-slides

Tigmint: Correct Misassemblies Using Linked Reads From Large Molecules

tldr

Simplified and community-driven man pages

tupper

Tupper's self-referential formula

uniqtag

Abbreviate strings to short, unique identifiers

uniqtag-data

Supplementary data for the UniqTag paper

uniqtag-paper

UniqTag: Content-derived unique and stable identifiers for gene annotation

uniqtag-slides

UniqTag: Content-derived unique and stable identifiers for gene annotation

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

white-spruce-organelles-paper

:evergreen_tree: Organellar Genomes of White Spruce (Picea glauca)

white-spruce-organelles-poster

null

wiki

My notes

xml-patch-make

XML patch allowing GNU make to output the workflow as XML

Commits To