sjackman
I am a computational biologist (PhD), a developer of Cell Ranger and Homebrew, an open-source programmer, an avid traveller, a singer, and an enthusiastic cook.
@10xGenomicsVancouver, Canada
Pinned Repositories
abyss
:microscope: Assemble large genomes using short reads
tigmint
⛓ Correct misassemblies using linked AND long reads
homebrew-bio
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
GFA-spec
Graphical Fragment Assembly (GFA) Format Specification
brew
🍺 The missing package manager for macOS (or Linux)
docker-bio
Docker images of bioinformatics software
dotfiles
~/.*
fastascripts
Manipulate FASTA files
lambdar
ƛR: Run R on AWS Lambda
uniqtag
Abbreviate strings to short, unique identifiers
sjackman's Repositories
sjackman/minitig
Assemble short reads into contigs using minimizers
sjackman/abyss-drosophila-melanogaster
:microscope: Assemble Drosophila melanogaster with ABySS
sjackman/linuxbrew-slides
Linuxbrew and Homebrew-Science
sjackman/genometools
GenomeTools genome analysis system.
sjackman/ggplot2-tutorial
Teaching materials for the R package ggplot2
sjackman/makefile-slides
:microscope: Automating Data Analysis Pipelines
sjackman/assembly-slides
Genome sequence assembly slides
sjackman/bamtools
C++ API & command-line toolkit for working with BAM data
sjackman/hackseq_2017_project_6
ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads
sjackman/linuxbrew-paper
:beer::penguin: Linuxbrew Enables Repeatable Cross-Platform Scientific Software Installation
sjackman/picea-sitchensis-organelles-poster
:evergreen_tree: Organellar Genomes of Sitka Spruce (Picea sitchensis): Assembly and Annotation
sjackman/salmon
Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments
sjackman/abyss2-slides
ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter
sjackman/arcs
Scaffold genome sequence assemblies using 10x Genomics data
sjackman/awesome-10x-genomics
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
sjackman/biomake
GNU-Make-like utility for managing builds and complex workflows
sjackman/distroless
🥑 Language focused docker images, minus the operating system.
sjackman/giab-slides
Assembling the Genome in a Bottle sequencing data with ABySS
sjackman/homebrew-sandbox
A testing ground for the Brewsci organization
sjackman/homebrew-science-deprecated
:microscope: Scientific formulae for the Homebrew package manager
sjackman/LINKS
Long Interval Nucleotide K-mer Scaffolder
sjackman/lobstr-code
lobSTR: a short tandem repeat profiler for next generation sequencing data
sjackman/miller
Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON
sjackman/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
sjackman/ntCard
Estimating k-mer coverage histogram of genomics data
sjackman/quast
Genome assembly evaluation tool
sjackman/sga
de novo sequence assembler using string graphs
sjackman/squeakr
Squeakr: An Exact and Approximate k -mer Counting System
sjackman/sra-tools
SRA Tools
sjackman/xml-patch-make
XML patch allowing GNU make to output the workflow as XML