BenLangmead/bowtie

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Created over 11 years ago
Updated about 2 years ago

BenLangmead/bowtie

BenLangmead

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An ultrafast memory-efficient short read aligner

Bowtie: http://bowtie-bio.sf.net

 - See AUTHORS for information about who wrote Bowtie and its various
   components.
 - See LICENSE for license information.
 - See MANUAL for detailed information on how to use Bowtie.
 - See NEWS for information about changes in this and previous versions
   of Bowtie.
 - See TUTORIAL for a quick example to get you started with Bowtie.

bowtie2

A fast and sensitive gapped read aligner

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

comp-genomics-class

Code and examples for JHU Computational Genomics class

Jupyter Notebook

c-cpp-notes

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

langmead-lab

Publicly-visible Langmead Lab resources

aws-indexes

Catalog of genomic indexes freely available from public clouds

crossbow

Variant calling from sequence reads using cloud computing

qtip

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

seq-frontiers-class

Code, examples, reading list for JHU Frontiers of Sequencing Data Analysis class

myrna

Cloud-scale differential expression for RNA-seq

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"

bsmooth-align

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

ads1-hw-examples

How some homework solutions should work on some small examples

jhu-compute

Resources to help use JHU's compute resources

sra-example

percy

Scripts for starting permanent, lightweight EC2 instances

public-seq-data

Scripts, manifests, etc for grabbing and lightly analyzing public data

recount-docker

Dockerization of recount and its R/Bioconductor dependencies

bowtie-dev

jupyter-all

Jupyter environment with various language kernels already installed

cgsi18

Scripts for downloading and querying raw Snaptron data

docker-oss

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