Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3607606?pdf=render |
| _version_ | 1819042099359645696 |
|---|---|
| author | Richard M Leggett Ricardo H Ramirez-Gonzalez Walter Verweij Cintia G Kawashima Zamin Iqbal Jonathan D G Jones Mario Caccamo Daniel Maclean |
| author_facet | Richard M Leggett Ricardo H Ramirez-Gonzalez Walter Verweij Cintia G Kawashima Zamin Iqbal Jonathan D G Jones Mario Caccamo Daniel Maclean |
| author_sort | Richard M Leggett |
| collection | DOAJ |
| description | Single Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism detection relies on having a reference genome to which reads can be aligned and variants detected. We present Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence. Bubbleparse uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively. We show that the Bubbleparse algorithm is sensitive and can detect many polymorphisms quickly and that it performs well when compared with polymorphism detection methods based on alignment to a reference in Arabidopsis thaliana. We show that the heuristic can be used to maximise the number of true polymorphisms returned, and with a proof-of-principle experiment show that Bubbleparse is very effective on data from unsequenced wild relatives of potato and enabled us to identify disease resistance linked genes quickly and easily. |
| first_indexed | 2024-12-21T09:35:30Z |
| format | Article |
| id | doaj.art-ffe763b8f7e34d909dfad1590c2ff99e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T09:35:30Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ffe763b8f7e34d909dfad1590c2ff99e2022-12-21T19:08:39ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0183e6005810.1371/journal.pone.0060058Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.Richard M LeggettRicardo H Ramirez-GonzalezWalter VerweijCintia G KawashimaZamin IqbalJonathan D G JonesMario CaccamoDaniel MacleanSingle Nucleotide Polymorphisms are invaluable markers for tracing the genetic basis of inheritable traits and the ability to create marker libraries quickly is vital for timely identification of target genes. Next-generation sequencing makes it possible to sample a genome rapidly, but polymorphism detection relies on having a reference genome to which reads can be aligned and variants detected. We present Bubbleparse, a method for detecting variants directly from next-generation reads without a reference sequence. Bubbleparse uses the de Bruijn graph implementation in the Cortex framework as a basis and allows the user to identify bubbles in these graphs that represent polymorphisms, quickly, easily and sensitively. We show that the Bubbleparse algorithm is sensitive and can detect many polymorphisms quickly and that it performs well when compared with polymorphism detection methods based on alignment to a reference in Arabidopsis thaliana. We show that the heuristic can be used to maximise the number of true polymorphisms returned, and with a proof-of-principle experiment show that Bubbleparse is very effective on data from unsequenced wild relatives of potato and enabled us to identify disease resistance linked genes quickly and easily.http://europepmc.org/articles/PMC3607606?pdf=render |
| spellingShingle | Richard M Leggett Ricardo H Ramirez-Gonzalez Walter Verweij Cintia G Kawashima Zamin Iqbal Jonathan D G Jones Mario Caccamo Daniel Maclean Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. PLoS ONE |
| title | Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. |
| title_full | Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. |
| title_fullStr | Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. |
| title_full_unstemmed | Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. |
| title_short | Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. |
| title_sort | identifying and classifying trait linked polymorphisms in non reference species by walking coloured de bruijn graphs |
| url | http://europepmc.org/articles/PMC3607606?pdf=render |
| work_keys_str_mv | AT richardmleggett identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT ricardohramirezgonzalez identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT walterverweij identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT cintiagkawashima identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT zaminiqbal identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT jonathandgjones identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT mariocaccamo identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs AT danielmaclean identifyingandclassifyingtraitlinkedpolymorphismsinnonreferencespeciesbywalkingcoloureddebruijngraphs |