sjackman/resume

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Created about 12 years ago
Updated over 4 years ago

sjackman/resume

sjackman

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PhD graduate in bioinformatics, programmer, engineer

lambdar

ƛR: Run R on AWS Lambda

fastascripts

Manipulate FASTA files

uniqtag

Abbreviate strings to short, unique identifiers

docker-bio

Docker images of bioinformatics software

makefile-example

An example of a data analysis pipeline using Make

assembly-graph

Compare assembly graph file formats

docker-linuxbrew

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

uniqtag-paper

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

abyss-scaffold-paper

Scaffolding a genome sequence assembly using ABySS

gfalint

Check a GFA file for syntax errors

homebrewr

An R package to install software using Homebrew

white-spruce-organelles-paper

🌲 Organellar Genomes of White Spruce (Picea glauca)

abyss-activity

ABySS learning activity

samskrit

Tools to manipulate SAM and BAM files

picea-sitchensis-mitochondrion

🧬🌲 Mitochondrial genome of Sitka spruce (Picea sitchensis)

orca-paper

🐳🍺🐧 ORCA: Genomics Research Container Architecture

picea-glauca-mitochondrion

Mitochondrial genome of white spruce (Picea glauca)

fastgtools

Tools to manipulate FASTG files

minitig

Assemble short reads into contigs using minimizers

dotfiles

linkage-map-slides

Scaffolding genome sequence assemblies using a linkage map

thesis

PhD Thesis: Efficient Assembly of Large Genomes

abyss-drosophila-melanogaster

🔬 Assemble Drosophila melanogaster with ABySS

linuxbrew-slides

Linuxbrew and Homebrew-Science

picea-sitchensis-mitochondrion-paper

🧬🌲 Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

OGDraw

A mirror of OrganellarGenomeDRAW

stat540-project

STAT 540 group project

abyss-pipeline

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

talr

TALR: Targeted Assembly of Linked Reads

makefile-slides

🔬 Automating Data Analysis Pipelines

mars-rover

🚀 Extraterrestrial DNA! 🚀

thesis-committee

PhD thesis committee presentation slides

distance-estimator-paper

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

10xgenomics-slides

Efficient Assembly of Large Genomes

assembly-slides

Genome sequence assembly slides

marmot-mitochondrion

Yellow-bellied marmot

konnector-vis

Visualize an ABySS-Konnector graph

scaffolding-coverage

Determine the required mate-pair coverage for scaffolding

picea-sitchensis-plastid

🌲 Annotate the plastid genome of Sitka spruce (Picea sitchensis)

linuxbrew-paper

🍺🐧 Linuxbrew Enables Repeatable Cross-Platform Scientific Software Installation

tigmint-data

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

snoove

Create a dendrogram from genome sequencing data

picea-sitchensis-mitochondrion-legacy

🌲 Mitochondrial genome of Sitka spruce (Picea sitchensis)

picea-sitchensis-organelles-poster

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

rewrite-git-history

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

picea-sitchensis-organelles-slides

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