Rapid and precise alignment of raw reads against redundant databases with KMA

BMC Bioinformatics
Philip T L C ClausenOle Lund

Abstract

As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another. In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates. The functionality of KMA was compared with SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, using both simulated data and a dataset of Escherichia coli mapped against resistance genes and core genome MLST alleles. KMA outperforms current methods with respect to both accuracy and speed, while using a comparable amount of memory. With KMA, it was possible map raw reads directly a...Continue Reading

References

Mar 1, 1970·Journal of Molecular Biology·S B Needleman, C D Wunsch
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
May 13, 2010·Briefings in Bioinformatics·Heng Li, Nils Homer
Feb 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Yonatan H GradWilliam P Hanage
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jul 12, 2012·The Journal of Antimicrobial Chemotherapy·Ea ZankariMette Voldby Larsen
Nov 26, 2014·Genome Medicine·Michael InouyeKathryn E Holt
Jul 2, 2016·The Journal of Antimicrobial Chemotherapy·Philip T L C ClausenOle Lund
Mar 7, 2017·Nature Methods·Rob PatroCarl Kingsford
May 4, 2017·PloS One·Thomas Nordahl PetersenThomas Sicheritz-Pontén
May 12, 2018·Bioinformatics·Heng Li

❮ Previous
Next ❯

Citations

Sep 22, 2019·Applied and Environmental Microbiology·Sofiya G ShevchenkoEvgeni V Sokurenko
Aug 9, 2020·The Journal of Infectious Diseases·Cedar L MitchellSteven R Meshnick
Jul 17, 2020·Journal of Clinical Microbiology·Anna Maria Malberg TetzschnerFlemming Scheutz
Mar 4, 2020·The Journal of Antimicrobial Chemotherapy·Ingrid Maria Cecilia RubinMette Pinholt
Aug 15, 2020·Scientific Reports·David F NieuwenhuijseMarion P G Koopmans
Sep 16, 2020·Scientific Reports·Bálint Ármin PatakiUNKNOWN SPS COMPARE ML-AMR group
Mar 18, 2020·Communicable Diseases Intelligence·Geoffrey W CoombsUNKNOWN Australian Group on Antimicrobial Resistance
Sep 26, 2020·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·Louise Gade DahlEva Møller Nielsen
Sep 30, 2020·Communicable Diseases Intelligence·Geoffrey W CoombsUNKNOWN Australian Group on Antimicrobial Resistance
Apr 10, 2019·BMC Biology·Vanessa R MarcelinoEdward C Holmes
Feb 29, 2020·BMC Genomics·Vanessa R MarcelinoTania C Sorrell
Sep 26, 2019·Frontiers in Public Health·Rene S HendriksenPatrick F McDermott
Aug 12, 2020·The Journal of Antimicrobial Chemotherapy·Valeria BortolaiaFrank M Aarestrup
Nov 2, 2019·Nucleic Acids Research·James J DavisRick Stevens
Oct 22, 2020·MSystems·Christian BrinchFrank M Aarestrup
Jan 9, 2021·Briefings in Bioinformatics·Tao HuWeifeng Shi
Jan 17, 2021·Scientific Reports·Josephine E S StrangeFrank M Aarestrup
Jan 24, 2021·Briefings in Bioinformatics·Dropen ShekaPaul M K Gordon
Feb 7, 2021·Current Biology : CB·Cintia IhaHeroen Verbruggen
Dec 29, 2020·Frontiers in Microbiology·Delphine GirlichThierry Naas
Nov 27, 2020·Frontiers in Genetics·Madangchanok ImchenVasco Azevedo

❮ Previous
Next ❯

Software Mentioned

MGmapper
BEDTools
MEM
Salmon
ResFinder
Minimap2 SAMtools
Minimap2
SRST2
BLAST
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.