Optimizing performance of GATK workflows using Apache Arrow In-Memory data framework.

BMC Genomics
Tanveer AhmadH Peter Hofstee

Abstract

Immense improvements in sequencing technologies enable producing large amounts of high throughput and cost effective next-generation sequencing (NGS) data. This data needs to be processed efficiently for further downstream analyses. Computing systems need this large amounts of data closer to the processor (with low latency) for fast and efficient processing. However, existing workflows depend heavily on disk storage and access, to process this data incurs huge disk I/O overheads. Previously, due to the cost, volatility and other physical constraints of DRAM memory, it was not feasible to place large amounts of working data sets in memory. However, recent developments in storage-class memory and non-volatile memory technologies have enabled computing systems to place huge data in memory to process it directly from memory to avoid disk I/O bottlenecks. To exploit the benefits of such memory systems efficiently, proper formatted data placement in memory and its high throughput access is necessary by avoiding (de)-serialization and copy overheads in between processes. For this purpose, we use the newly developed Apache Arrow, a cross-language development framework that provides language-independent columnar in-memory data format fo...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 22, 1985·Science·D J Lipman, W R Pearson
May 29, 2000·Trends in Genetics : TIG·P RiceA Bleasby
Apr 5, 2002·Genome Research·W James Kent
Oct 22, 2004·Nature·UNKNOWN International Human Genome Sequencing Consortium
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Feb 12, 2013·Nature Biotechnology·Kristian CibulskisGad Getz
May 9, 2014·Bioinformatics·Gregory G Faust, Ira M Hall
Feb 24, 2015·Bioinformatics·Artem TarasovPjotr Prins
May 11, 2018·Computational Biology and Chemistry·Ernst Joachim HoutgastZaid Al-Ars
May 17, 2018·Human Molecular Genetics·Martin O PollardManjinder S Sandhu
Jul 18, 2018·Nature Methods·Sangtae KimChristopher T Saunders
Sep 25, 2018·Nature Biotechnology·Ryan PoplinMark A DePristo
Feb 14, 2019·PloS One·Charlotte HerzeelWilfried Verachtert

❮ Previous
Next ❯

Datasets Mentioned

BETA
NA12878
SRR622461

Methods Mentioned

BETA
exome sequencing

Software Mentioned

VarDict
LoFreq
Dataframes
VarScan
Apache Spark
Rust
SAMtools
elPrep
CUDA
Freebayes

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2021 Meta ULC. All rights reserved