sjackman/10xgenomics-slides

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sjackman/10xgenomics-slides

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Efficient Assembly of Large Genomes

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

resume

PhD graduate in bioinformatics, programmer, engineer

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

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