BenLangmead

Benjamin Langmead's starred repositories

ipython

Official repository for IPython itself. Other repos in the IPython organization contain things like the website, documentation builds, etc.

Language:PythonBSD-3-Clause16232 744 7344

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Language:CGPL-3.01508 108 304

elephant-bird

Twitter's collection of LZO and Protocol Buffer-related Hadoop, Pig, Hive, and HBase code.

Language:JavaApache-2.01139 189 139

bedtools2

bedtools - the swiss army knife for genome arithmetic

Language:CMIT919 58 831

gemini

a lightweight db framework for exploring genetic variation.

Language:PythonMIT318 44 568

nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

Language:C++BSD-3-Clause204 29 36

dashing

Fast and accurate genomic distances using HyperLogLog

Language:C++GPL-3.0160 11 64

bedtools

A powerful toolset for genome arithmetic.

Language:C++GPL-2.0139 20 117

Lighter

Fast and memory-efficient sequencing error corrector

Language:C++GPL-3.092 10 32

scallop

Scallop is a reference-based transcriptome assembler for RNA-seq

Language:C++BSD-3-Clause88 16 38

quip

Compressing next-generation sequencing data with extreme prejudice.

Language:CBSD-3-Clause78 5 30

rail

Scalable RNA-seq analysis

Language:PythonNOASSERTION73 11 53

Arioc

Arioc: GPU-accelerated DNA short-read alignment

BSD-3-Clause56 6 32

spumoni

Pan-Genomic Matching Statistics

Language:C++GPL-3.045 5 7

samovar

Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters

Language:PythonMIT24 4 3

derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data

Language:RMIT22 7 13

dandd

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

Language:PythonMIT21 4 2

boiler

Boiler: a software tool for highly efficient, lossy compression of RNA-seq alignments

Language:PythonMIT13 30

codoc

CODOC project

Language:Java6 1 1