Frank Austin Nothaft

Login: fnothaft

Company: Databricks

Location: Oakland, CA

Bio: null

Blog: http://www.fnothaft.net

Blog: http://www.fnothaft.net

Member of

1. AMPLab at UC Berkeley
2. Big Data Genomics

Repositories

adam

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

adam-fs-benchmarks

null

adam-queries

Small queries to run on ADAM for GDA.

adam-regression

Regression testing setup for ADAM.

adam-snpeff

SnpEff on Spark via ADAM pipe APIs

ananas

null

avocado

A Variant Caller, Distributed

bdg-formats

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

bdg-recipes

Recipes using BDG projects. Apache 2 licensed.

bdg-services

Utility classes for wrapping services or other interfaces around a Spark/ADAM cluster.

bdg-utils

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

BigData_2015

null

bigdatagenomics.github.io

Web Site for the Big Data Genomics Group

bits

Firebox Benchmarks

blog

null

cannoli

A little, Apache 2 licensed pipe.

cannoli-1

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

cgcloud

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

cgl-docker-lib

null

cloud-scale-bwamem

null

conductor

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

copier

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

corretto

Read error correction utilities.

deca

Distributed exome CNV analyzer. Apache 2 licensed.

docker-images

Miscellaneous Docker images.

docs

My writings.

eggo

Ready-to-go Parquet-formatted public 'omics datasets

fig

A tool for Finding Interesting variants that modify regulatory Grammar.

fnothaft.github.io

Personal website.

gatk

Official code repository for GATK versions 4 and up

gatk-whole-genome-pipeline

End to end pipeline for calling variants against an entire genome

gnocchi

null

gnocchi-1

null

gt

null

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.

hadoop-interfaces

null

homebrew-science

Scientific formulae for the Homebrew package manager

htsjdk

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

IEEE_TBD_2016

null

incubator-parquet-mr

Mirror of Apache Parquet

jsr203-hadoop

A Java NIO file system provider for HDFS

jsr203-s3a

null

mango

Visualization tools for genomic data. Apache 2 licensed.

mmtf-spark

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

mmtf-workshop-2017

Structural Bioinformatics Training Workshop & Hackathon 2017

PacMin

Assembler for PacBio reads. Apache 2 licensed.

parquet-mr

Java readers/writers for Parquet columnar file formats to use with Map-Reduce

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

qc-metrics

Read and variant metrics, useable for pipeline quality control purposes. Apache 2 licensed.

ReadTaskTeam

null

RefVariationTaskTeam

Work on data models and APIs for graph structures that represent the human reference genome plus common human genetic variants. Includes mapping to a reference genome, and standardization of the mechanism for referring to variants.

RNAdam

An RNA fusion transcript pipeline built on top of ADAM. Apache 2 licensed.

sequence-graphs

Implementation of the Sequence Graphs data model

server

A reference implementation of the APIs defined in the schemas repository.

siren-release

Public version of the SiRen project

snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data

snappea

Parallel alignment using SNAP on ADAM. Apache 2 licensed.

snark

A nested vector library for Scala.

spark-bam

Load genomic BAM files using Apache Spark

SparkMontage

null

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.

toil-lib

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

toil-scripts

null

toil-wdl-api

Exemplar API that mediates Toil with a WDL front-end and workflow tracking.

training

Training materials for Strata, AMP Camp, etc

VariantDB_Challenge

Finding a scalable alternative to the VCF File for genomics analysis

vcfimp

Strict VCF Parser

workflows

Toil workflows for bigdatagenomics tools. Apache 2 licensed.

xASSEMBLEx

An ADAM/GraphX based assembler. Apache 2 licensed.

Commits To