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bayolau's Projects

bwa icon bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

cpp_cmake_boost_bio icon cpp_cmake_boost_bio

reusable, self-contained c++/cmake/boost infrastructure for quick bioinformatics development

daligner icon daligner

Find all significant local alignments between reads

damapper icon damapper

Long read to reference genome mapping tool

damasker icon damasker

Module to determine where repeats are and make soft-masks of said

discovar icon discovar

unofficial GIT tracking of the public release of DISCOVAR, whose repo has not been released

discovardenovo icon discovardenovo

unofficial GIT tracking of the public release of DISCOVAR-denovo by Broad Institute's CRD team

freebayes icon freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

graphmap icon graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html

htsjdk icon htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

htslib icon htslib

C library for high-throughput sequencing data formats

libstatgen icon libstatgen

Useful set of classes for creating statistical genetic programs.

longislnd icon longislnd

LongISLND - Long In silico Sequencing of Lengthy and Noisy Datatypes

miniasm icon miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minimap icon minimap

Experimental tool to find approximate mapping positions between long sequences

nucleo icon nucleo

Workflow that creates all the BAM files for the cfDNA assay based FASTQ file at MSK

pysam icon pysam

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

samtools icon samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

seqan icon seqan

SeqAn's official repository.

statsmodels icon statsmodels

Statsmodels: statistical modeling and econometrics in Python

today-scripts icon today-scripts

A widget for running scripts in the Today View in OS X Yosemite's Notification Center

varsim icon varsim

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

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