Comparison of Sequencing Utility Programs

Aronesty, Erik

Comparison of Sequencing Utility Programs

Erik Aronesty^*

Expression Analysis, A Quintiles Company, Durham, NC, USA

Article Information

Identifiers and Pagination:

Year: 2013
Volume: 7
First Page: 1
Last Page: 8
Publisher ID: TOBIOIJ-7-1
DOI: 10.2174/1875036201307010001

Article History:

Received Date: 01/11/2012
Revision Received Date: 15/11/2012
Acceptance Date: 17/11/2012
Electronic publication date: 31/01/2013
Collection year: 2013

Article Metrics

CrossRef Citations:

Total Statistics:

Full-Text HTML Views: 6317
Abstract HTML Views: 6043
PDF Downloads: 2089
Total Views/Downloads: 14449

Unique Statistics:

Full-Text HTML Views: 3368
Abstract HTML Views: 3391
PDF Downloads: 1702
Total Views/Downloads: 8461

© 2013 Erik Aronesty

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

^* Address correspondence to this author at the Expression Analysis, a Quintiles Company, Durham, NC, USA; Tel: 919-287-4011; E-mail: erik.aronesty@quintiles.com

High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly.

Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools to similar open-source utilities, both in terms of resource efficiency, and effectiveness.

Keywords: Sequencing, utilities, Illumina, clipping, ngs and next-generation.

Download PDF Next Article

Track Your Manuscript
Enter Correct Manuscript Reference Number:

Submit Reference Number
Published Contents

Feng Cheng

Department of Pharmaceutical Science
University of South Florida
Tampa, FL
USA

View Biography

View Editorial Board

About the Journal
The Open Bioinformatics Journal
ISSN: 1875-0362
Volume: 16, 2023

Download Flyer
Processing Time: Average publication time is 18 days between the final acceptance of revised manuscript and its publication
READ MORE

Press Release
Bentham Open Welcomes Sultan Idris University of Education (UPSI) as Institutional Member

Description:
Bentham Open is pleased to welcome Sultan Idris University of Education (UPSI), Malaysia as Institutional Member. The partnership allows the researchers from the university to publish their research under an Open Access license with specified fee discounts. Bentham Open welcomes institutions and organizations from world over to join as Institutional Member and avail a host of benefits for their researchers.

Sultan Idris University of Education (UPSI) was established in 1922 and was known as the first Teacher Training College of Malaya. It is known as one of the oldest universities in Malaysia. UPSI was later upgraded to a full university institution on 1 May, 1997, an upgrade from their previous college status. Their aim to provide exceptional leadership in the field of education continues until today and has produced quality graduates to act as future educators to students in the primary and secondary level.

Bentham Open publishes a number of peer-reviewed, open access journals. These free-to-view online journals cover all major disciplines of science, medicine, technology and social sciences. Bentham Open provides researchers a platform to rapidly publish their research in a good-quality peer-reviewed journal. All peer-reviewed accepted submissions meeting high research and ethical standards are published with free access to all.

Ministry Of Health, Jordan joins Bentham Open as Institutional Member

Description:
Bentham Open is pleased to announce an Institutional Member partnership with the Ministry of Health, Jordan. The partnership provides the opportunity to the researchers, from the university, to publish their research under an Open Access license with specified fee concessions. Bentham Open welcomes institutions and organizations from the world over to join as Institutional Member and avail a host of benefits for their researchers.

The first Ministry of Health in Jordan was established in 1950. The Ministry began its duties in 1951, the beginning of the health development boom in Jordan. The first accomplishment was the establishment of six departments in the districts headed by a physician and under the central administration of the Ministry. The Ministry of Health undertakes all health affairs in the Kingdom and its accredited hospitals include AL-Basheer Hospital, Zarqa Governmental Hospital, University of Jordan Hospital, Prince Hashem Military Hospital and Karak Governmental Hospital.

Bentham Open publishes a number of peer-reviewed, open access journals. These free-to-view online journals cover all major disciplines of science, medicine, technology and social sciences. Bentham Open provides researchers a platform to rapidly publish their research in a good-quality peer-reviewed journal. All peer-reviewed, accepted submissions meeting high research and ethical standards are published with free access to all.

Porto University joins Bentham Open as Institutional Member

Description:
Bentham Open is pleased to announce an Institutional Member partnership with the Porto University, Faculty of Dental Medicine (FMDUP). The partnership provides the opportunity to the researchers, from the university, to publish their research under an Open Access license with specified fee concessions. Bentham Open welcomes institutions and organizations from world over to join as Institutional Member and avail a host of benefits for their researchers.

The Porto University was founded in 1911. Porto University create scientific, cultural and artistic knowledge, higher education training strongly anchored in research, the social and economic valorization of knowledge and active participation in the progress of the communities in which it operates.

Bentham Open publishes a number of peer-reviewed, open access journals. These free-to-view online journals cover all major disciplines of science, medicine, technology and social sciences. Bentham Open provides researchers a platform to rapidly publish their research in a good-quality peer-reviewed journal. All peer-reviewed accepted submissions meeting high research and ethical standards are published with free access to all.
Join Our Editorial Board

Description:
The Open Bioinformatics Journal is an Open Access online journal, which publishes research articles, reviews, letters, case reports and guest-edited single topic issues in all areas of bioinformatics and computational biology. Bentham Open ensures speedy peer review process and accepted papers are published within 2 weeks of final acceptance.

The Open Bioinformatics Journal is committed to ensuring high quality of research published. We believe that a dedicated and committed team of editors and reviewers make it possible to ensure the quality of the research papers. The overall standing of a journal is in a way, reflective of the quality of its Editor(s) and Editorial Board and its members.

The Open Bioinformatics Journal is seeking energetic and qualified researchers to join its editorial board team as Editorial Board Members or reviewers.

The essential criteria to become Editorial Board Members of The Open Bioinformatics Journal are as follows:
1. Experience in bioinformatics and computational biology with an academic degree.
2. At least 20 publication records of articles and /or books related to the field of bioinformatics and computational biology or in a specific research field.
3. Proficiency in English language.
The Roles of Editorial Board Member are to:
1. Offer advice on journals’ policy and scope.
2. Submit or solicit at least one article for the journal annually.
3. Contribute and/or solicit Guest Edited thematic issues to the journal in a hot area (at least one thematic issue every two years).
4. Peer-review of articles for the journal, which are in the area of expertise (2 to 3 times per year).
If you are interested in becoming our Editorial Board member, please submit the following information to info@benthamopen.net. We will respond to your inquiry shortly.

Email subject: Editorial Board Member Application
1. Your name
2. Email address
3. Telephone
4. City, State, Country
5. Name of your institution
6. Department or Division
7. Website of institution
8. Your title or position
9. Your highest degree
10. Complete list of publications and h-index
11. Interested field(s)
Testimonials

"Open access will revolutionize 21^st century knowledge work and accelerate the diffusion of ideas and evidence that support just in time learning and the evolution of thinking in a number of disciplines."
. —Daniel Pesut. (Indiana University School of Nursing, USA).

"It is important that students and researchers from all over the world can have easy access to relevant, high-standard and timely scientific information. This is exactly what Open Access Journals provide and this is the reason why I support this endeavor."
. —Jacques Descotes. (Centre Antipoison-Centre de Pharmacovigilance, France).

"Publishing research articles is the key for future scientific progress. Open Access publishing is therefore of utmost importance for wider dissemination of information, and will help serving the best interest of the scientific community."
. —Patrice Talaga. (UCB S.A., Belgium).

"Open access journals are a novel concept in the medical literature. They offer accessible information to a wide variety of individuals, including physicians, medical students, clinical investigators, and the general public. They are an outstanding source of medical and scientific information."
. —Jeffrey M. Weinberg. (St. Luke's-Roosevelt Hospital Center, USA).

"Open access journals are extremely useful for graduate students, investigators and all other interested persons to read important scientific articles and subscribe scientific journals. Indeed, the research articles span a wide range of area and of high quality. This is specially a must for researchers belonging to institutions with limited library facility and funding to subscribe scientific journals."
. —Debomoy K. Lahiri. (Indiana University School of Medicine, USA).

"Open access journals represent a major break-through in publishing. They provide easy access to the latest research on a wide variety of issues. Relevant and timely articles are made available in a fraction of the time taken by more conventional publishers. Articles are of uniformly high quality and written by the world's leading authorities."
. —Robert Looney. (Naval Postgraduate School, USA).

"Open access journals have transformed the way scientific data is published and disseminated: particularly, whilst ensuring a high quality standard and transparency in the editorial process, they have increased the access to the scientific literature by those researchers that have limited library support or that are working on small budgets."
. —Richard Reithinger. (Westat, USA).

"Not only do open access journals greatly improve the access to high quality information for scientists in the developing world, it also provides extra exposure for our papers."
. —J. Ferwerda. (University of Oxford, UK).

"Open Access 'Chemistry' Journals allow the dissemination of knowledge at your finger tips without paying for the scientific content."
. —Sean L. Kitson. (Almac Sciences, Northern Ireland).

"In principle, all scientific journals should have open access, as should be science itself. Open access journals are very helpful for students, researchers and the general public including people from institutions which do not have library or cannot afford to subscribe scientific journals. The articles are high standard and cover a wide area."
. —Hubert Wolterbeek. (Delft University of Technology, The Netherlands).

"The widest possible diffusion of information is critical for the advancement of science. In this perspective, open access journals are instrumental in fostering researches and achievements."
. —Alessandro Laviano. (Sapienza - University of Rome, Italy).

"Open access journals are very useful for all scientists as they can have quick information in the different fields of science."
. —Philippe Hernigou. (Paris University, France).

"There are many scientists who can not afford the rather expensive subscriptions to scientific journals. Open access journals offer a good alternative for free access to good quality scientific information."
. —Fidel Toldrá. (Instituto de Agroquimica y Tecnologia de Alimentos, Spain).

"Open access journals have become a fundamental tool for students, researchers, patients and the general public. Many people from institutions which do not have library or cannot afford to subscribe scientific journals benefit of them on a daily basis. The articles are among the best and cover most scientific areas."
. —M. Bendandi. (University Clinic of Navarre, Spain).

"These journals provide researchers with a platform for rapid, open access scientific communication. The articles are of high quality and broad scope."
. —Peter Chiba. (University of Vienna, Austria).

"Open access journals are probably one of the most important contributions to promote and diffuse science worldwide."
. —Jaime Sampaio. (University of Trás-os-Montes e Alto Douro, Portugal).

"Open access journals make up a new and rather revolutionary way to scientific publication. This option opens several quite interesting possibilities to disseminate openly and freely new knowledge and even to facilitate interpersonal communication among scientists."
. —Eduardo A. Castro. (INIFTA, Argentina).

"Open access journals are freely available online throughout the world, for you to read, download, copy, distribute, and use. The articles published in the open access journals are high quality and cover a wide range of fields."
. —Kenji Hashimoto. (Chiba University, Japan).

"Open Access journals offer an innovative and efficient way of publication for academics and professionals in a wide range of disciplines. The papers published are of high quality after rigorous peer review and they are Indexed in: major international databases. I read Open Access journals to keep abreast of the recent development in my field of study."
. —Daniel Shek. (Chinese University of Hong Kong, Hong Kong).

"It is a modern trend for publishers to establish open access journals. Researchers, faculty members, and students will be greatly benefited by the new journals of Bentham Science Publishers Ltd. in this category."
. —Jih Ru Hwu. (National Central University, Taiwan).

RESEARCH ARTICLE

Comparison of Sequencing Utility Programs

Article Information

Identifiers and Pagination:

Article History:

Article Metrics

CrossRef Citations:

Total Statistics:

Unique Statistics:

Abstract

Track Your Manuscript

Published Contents

About the Editor

About the Journal

The Open Bioinformatics Journal

Press Release

Bentham Open Welcomes Sultan Idris University of Education (UPSI) as Institutional Member

Ministry Of Health, Jordan joins Bentham Open as Institutional Member

Porto University joins Bentham Open as Institutional Member

Join Our Editorial Board

Testimonials