Long fragments achieve lower base quality in Illumina paired-end sequencing

Scientific Reports
Ge TanHubert Rehrauer

Abstract

Illumina's technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Sequencing runs typically generate millions of reads in which the vast majority of the reads has an average error rate below 1/1000. However, some paired-end sequencing data show the presence of a subpopulation of reads where the second read (R2) has lower average qualities. We show that the fragment length is a major driver of increased error rates in the R2 reads. Fragments above 500 nt tend to yield lower base qualities and higher error rates than shorter fragments. We use publicly available Illumina data to demonstrate that the fragment length dependency of the R2 read qualities exists in various library protocols, in different labs and using different sequencer models. Our finding extends the understanding of the Illumina read quality and has implications on error models for Illumina reads. It also sheds a light on the importance of controlling the fragment size during library preparation.

References

Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Apr 17, 2010·Nucleic Acids Research·Kasper D HansenSandrine Dudoit
May 18, 2011·Nucleic Acids Research·Kensuke NakamuraShigehiko Kanaya
Nov 22, 2011·BMC Bioinformatics·Frazer MeachamLior Pachter
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 14, 2013·BMC Bioinformatics·Manuel AllhoffTobias Marschall
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Dec 19, 2015·BMC Bioinformatics·Soumitra Pal, Srinivas Aluru
May 18, 2016·Nature Reviews. Genetics·Sara GoodwinW Richard McCombie
Jun 21, 2016·Nature Reviews. Genetics·Merly EscalonaDavid Posada
Sep 28, 2016·Journal of Biomolecular Techniques : JBT·Leigh J ManleyStuart S Levine

❮ Previous
Next ❯

Citations

Feb 21, 2021·Genome Biology·Stephan Schmeing, Mark D Robinson
Mar 20, 2021·Scientific Reports·Maximiliano Martín AballayGerardo Sánchez
Aug 7, 2021·Scientific Reports·Piyush MathurPankaj Yadav
Aug 28, 2020·Environmental Science & Technology·Jackson F PreussAlexandro M Tozetti
Dec 8, 2021·Proceedings of the National Academy of Sciences of the United States of America·Stephanie C Y YuY M Dennis Lo

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq
DNA-seq
exome sequencing

Software Mentioned

SRA
Illumina BaseSpace
BaseSpace
gam
BWA
Illumina BaseSpace SRA
Ensembl
Illumina
Trimmomatic
samtools

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.