fnothaft/v2g_data
Gene to variant functional dataset workflows
Repositories
fnothaft/fnothaft.github.io
Personal website.
fnothaft/docs
My writings.
fnothaft/glow
An open-source toolkit for large-scale genomic analysis
fnothaft/xASSEMBLEx
An ADAM/GraphX based assembler. Apache 2 licensed.
fnothaft/TypeSeqHPV
NCI CGR laboratory HPV typing analysis workflows
fnothaft/adam
A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.
fnothaft/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.
fnothaft/VariantDB_Challenge
Finding a scalable alternative to the VCF File for genomics analysis
fnothaft/gatk
Official code repository for GATK versions 4 and up
fnothaft/spark-bam
Load genomic BAM files using Apache Spark
fnothaft/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.
fnothaft/jsr203-s3a
fnothaft/workflows
Toil workflows for bigdatagenomics tools. Apache 2 licensed.
fnothaft/parquet-mr
Java readers/writers for Parquet columnar file formats to use with Map-Reduce
fnothaft/snappea
Parallel alignment using SNAP on ADAM. Apache 2 licensed.
fnothaft/mmtf-workshop-2017
Structural Bioinformatics Training Workshop & Hackathon 2017
fnothaft/mmtf-spark
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
fnothaft/copier
Apache Spark-based tool for downloading a list of URLs. Apache 2 licensed.
fnothaft/cgl-docker-lib
fnothaft/jsr203-hadoop
A Java NIO file system provider for HDFS
fnothaft/avocado
A Variant Caller, Distributed
fnothaft/cannoli-1
Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.
fnothaft/gnocchi-1
fnothaft/cloud-scale-bwamem
fnothaft/deca
Distributed exome CNV analyzer. Apache 2 licensed.
fnothaft/BigData_2015
fnothaft/docker-images
Miscellaneous Docker images.
fnothaft/adam-snpeff
SnpEff on Spark via ADAM pipe APIs
fnothaft/fig
A tool for Finding Interesting variants that modify regulatory Grammar.