Benjamin Langmead (@BenLangmead)
github

BenLangmead

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Top repositories

1

bowtie2

A fast and sensitive gapped read aligner
C++
629
star
2

ads1-notebooks

Copies of notebooks used in the practical sessions for Algorithms for DNA Sequencing
347
star
3

ads1-slides

Slides for Algorithms for DNA Sequencing Coursera class
296
star
4

comp-genomics-class

Code and examples for JHU Computational Genomics class
Jupyter Notebook
284
star
5

bowtie

An ultrafast memory-efficient short read aligner
C++
255
star
6

c-cpp-notes

Lecture notes and example code for teaching C & C++
Python
234
star
7

langmead-lab

Publicly-visible Langmead Lab resources
58
star
8

aws-indexes

Catalog of genomic indexes freely available from public clouds
Python
52
star
9

crossbow

Variant calling from sequence reads using cloud computing
Perl
38
star
10

qtip

Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
C++
24
star
11

seq-frontiers-class

Code, examples, reading list for JHU Frontiers of Sequencing Data Analysis class
24
star
12

myrna

Cloud-scale differential expression for RNA-seq
Perl
15
star
13

bowtie-majref

Scripts related to building major-allele references for Bowtie and Bowtie 2
Shell
11
star
14

bowtie-scaling

Experiments for "Scaling read aligners to hundreds of threads on general-purpose processors"
Python
11
star
15

bsmooth-align

Alignment of bisulfite sequence reads and tabulation of read-level methylation measurements
C++
10
star
16

ads1-hw-examples

How some homework solutions should work on some small examples
9
star
17

jhu-compute

Resources to help use JHU's compute resources
3
star
18

sra-example

C++
2
star
19

percy

Scripts for starting permanent, lightweight EC2 instances
Python
2
star
20

public-seq-data

Scripts, manifests, etc for grabbing and lightly analyzing public data
Python
1
star
21

recount-docker

Dockerization of recount and its R/Bioconductor dependencies
R
1
star
22

bowtie-dev

Shell
1
star
23

jupyter-all

Jupyter environment with various language kernels already installed
Dockerfile
1
star
24

cgsi18

Scripts for downloading and querying raw Snaptron data
HTML
1
star
25

docker-oss

Automatic compatibility tests, e.g. to learn which OS versions a binary can be run on
Shell
1
star