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ads1-hw-examples

How some homework solutions should work on some small examples

ads1-notebooks

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

ads1-slides

Slides for Algorithms for DNA Sequencing Coursera class

aws-indexes

Catalog of genomic indexes freely available from public clouds

bioconda-recipes

Conda recipes for the bioconda channel.

bonsai

Bonsai: Ultrafast, flexible taxonomic analysis and classification

bounter

Efficient Counter that uses a limited (bounded) amount of memory regardless of data size.

bowtie

An ultrafast memory-efficient short read aligner

bowtie-dev

bowtie-majref

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

bowtie-scaling

Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"

bowtie-site

Files behind the Bowtie website

bowtie2

A fast and sensitive gapped read aligner

bsmooth-align

Alignment of bisulfite sequence reads and tabulation of read-level methylation measurements

bt2-cloudbench

Scripts for running Bowtie 2 tests on many different cloud instances

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

bwtool

A tool for bigWig files.

c-cpp-notes

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

cgsi18

Scripts for downloading and querying raw Snaptron data

circleci-test

clion-experiments

Experimenting with CLion for teaching

cloud-review

comp-genomics-class

Code and examples for JHU Computational Genomics class

crossbow

Variant calling from sequence reads using cloud computing

cufflinks

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

docker-oss

Automatic compatibility tests, e.g. to learn which OS versions a binary can be run on