Giters
Frank Austin Nothaft (fnothaft)

fnothaft

Geek Repo

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Company:@translating-science

Location:Oakland, CA

Home Page:http://www.fnothaft.net

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Organizations
amplab
bigdatagenomics

Frank Austin Nothaft's repositories

docs

My writings.

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adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

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avocado

A Variant Caller, Distributed

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copier

Apache Spark-based tool for downloading a list of URLs. Apache 2 licensed.

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bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

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bdg-utils

General (non-omics) code used across BDG products. Apache 2 licensed.

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bigdatagenomics.github.io

Web Site for the Big Data Genomics Group

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cannoli-1

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

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cgcloud

Image and VM management for Jenkins, Spark and Mesos clusters in EC2

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cgl-docker-lib

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cloud-scale-bwamem

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conductor

Efficient, distributed downloads of large files from S3 to HDFS using Spark.

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corretto

Read error correction utilities.

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deca

Distributed exome CNV analyzer. Apache 2 licensed.

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fnothaft.github.io

Personal website.

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gatk

Official code repository for GATK versions 4 and up

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glow

An open-source toolkit for large-scale genomic analysis

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gnocchi-1

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Hadoop-BAM

Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.

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jsr203-hadoop

A Java NIO file system provider for HDFS

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jsr203-s3a

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mango

Visualization tools for genomic data. Apache 2 licensed.

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mmtf-spark

Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

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mmtf-workshop-2017

Structural Bioinformatics Training Workshop & Hackathon 2017

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spark-bam

Load genomic BAM files using Apache Spark

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toil

Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.

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toil-lib

A common library for functions and tools used in toil-based pipelines

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TypeSeqHPV

NCI CGR laboratory HPV typing analysis workflows

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v2g_data

Gene to variant functional dataset workflows

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workflows

Toil workflows for bigdatagenomics tools. Apache 2 licensed.

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