BenLangmead

bowtie2

A fast and sensitive gapped read aligner

ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing

comp-genomics-class

Code and examples for JHU Computational Genomics class

bowtie

An ultrafast memory-efficient short read aligner

c-cpp-notes

Lecture notes and example code for teaching C & C++

aws-indexes

Catalog of genomic indexes freely available from public clouds

qtip

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities

myrna

Cloud-scale differential expression for RNA-seq

bowtie-majref

Scripts related to building major-allele references for Bowtie and Bowtie 2

percy

Scripts for starting permanent, lightweight EC2 instances

bonsai

Bonsai: Ultrafast, flexible taxonomic analysis and classification

cgsi18

Scripts for downloading and querying raw Snaptron data

jupyter-all

Jupyter environment with various language kernels already installed

kraken2

The second version of the Kraken taxonomic sequence classification system

moni

MONI: A Pangenomic Index for Finding MEMs

open-data-registry

A registry of publicly available datasets on AWS

recount-docker

Dockerization of recount and its R/Bioconductor dependencies

semesterly

Your Semester Made Easier | Course Scheduling & Social Tools for Students

bt2-cloudbench

Scripts for running Bowtie 2 tests on many different cloud instances

bwtool

A tool for bigWig files.

dashing

Fast and accurate genomic distances using HyperLogLog

dev-dandD

Tool to estimate deltas for sequence sets and answer questions about relative contribution

digest

digest-experiments

genome_info_curve

Genome Utility

inorder-site

kraken2-experiment-code

Code backing the results of the Kraken 2 paper

langmead-lab-web

Langmead lab website

pfbwt-f

Prefix Free Parsing Algorthim for building BWTs for genomic data

spumoni

Pan-Genomic Matching Statistics