SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

BMC Bioinformatics
David B BurdickJohn Boyle

Abstract

High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

References

Dec 7, 2006·Source Code for Biology and Medicine·Bruz Marzolf, Pamela Troisch
Jan 25, 2008·Nature·Helge Grosshans, Witold Filipowicz
Mar 29, 2008·Journal of Molecular Endocrinology·Marcel E DingerJohn S Mattick
Apr 23, 2008·Current Protocols in Bioinformatics·James TaylorAnton Nekrutenko
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 4, 2008·Nature Biotechnology·Hongkai JiWing H Wong
Nov 22, 2008·Science·John EidStephen Turner
Mar 7, 2009·BMC Bioinformatics·John BoyleIlya Shmulevich
Apr 21, 2009·Nature Genetics·Ryan J TaftJohn S Mattick
Jul 26, 2012·Bioinformatics·Valentina BoevaEmmanuel Barillot

❮ Previous
Next ❯

Methods Mentioned

BETA
Chip-Seq
RNA-Seq
to
support
ChIPSeq

Software Mentioned

Galaxy
Addama Robot
JSON
SLIMseq
Geospiza
JCR Java Content
Addama
ChIP
Seq Analysis Server
Genomatix Genome Analyzer

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.