A rapid algorithm to describe community structure using next generation amplicon sequencing data
(2015) KBK820 20151Pure and Applied Biochemistry
- Abstract
- Recent advances in the sequencing technology has led to an increasing pressure
on the computer programs used for analysing the sequence data. The programs
should be able to provide accurate analysis in a reasonable time span. 16S rRNA
analysis is performed by using PCR to amplify the 16S rRNA genes from bacteria
and archaea in a sample followed by sequencing of the amplicons. The result is
text files containing millions of short sequences. Those sequences are processed and
analysed using a variety of tools. Those tools are often only able to perform parts
of the analysis steps or require extensive knowledge and time to operate properly.
During this project a processing and analysis pipeline for 16S rRNA amplicon data
has been... (More) - Recent advances in the sequencing technology has led to an increasing pressure
on the computer programs used for analysing the sequence data. The programs
should be able to provide accurate analysis in a reasonable time span. 16S rRNA
analysis is performed by using PCR to amplify the 16S rRNA genes from bacteria
and archaea in a sample followed by sequencing of the amplicons. The result is
text files containing millions of short sequences. Those sequences are processed and
analysed using a variety of tools. Those tools are often only able to perform parts
of the analysis steps or require extensive knowledge and time to operate properly.
During this project a processing and analysis pipeline for 16S rRNA amplicon data
has been developed. It is able to take raw sequencing data, process it, analyse
it and return an overview of the community structure. The program has been
implemented on a server and can be accessed through a web interface where the
user simply provides a email address and uploads the data, requiring no previous
knowledge. The software has been compared to Qiime, one of the most widely used
pipelines for amplicon sequencing analysis, showing that it is able to produce a
similar taxonomic overview and estimates of the species richness and abundance.
It is designed to be further extended, and is planned to be open sourced, allowing
other programmers to contribute to its development in the future. In the moment
of writing, the pipeline can be accessed through following temporary link: http:
//130.235.244.91/Pipeline/. (Less) - Popular Abstract (Swedish)
- Ett snabbt program för automatiserad analys av mikroorganismsamhällen
Mikroorganismer finns överallt i vår omgivning. De lever i alla tänkbara miljöer, från i våra kroppar till i vårt dricksvatten. Olika organismer trivs under olika förhållanden. Vi kan studera vilka organismer som lever på en viss plats för att lära oss om deras omgivning. Men för att göra det måste vi ha rätt verktyg.
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/5105175
- author
- Willforss, Jakob LU
- supervisor
- organization
- course
- KBK820 20151
- year
- 2015
- type
- H2 - Master's Degree (Two Years)
- subject
- keywords
- amplicon sequencing, pipeline
- language
- English
- id
- 5105175
- date added to LUP
- 2015-03-02 17:49:32
- date last changed
- 2015-03-02 17:49:32
@misc{5105175, abstract = {{Recent advances in the sequencing technology has led to an increasing pressure on the computer programs used for analysing the sequence data. The programs should be able to provide accurate analysis in a reasonable time span. 16S rRNA analysis is performed by using PCR to amplify the 16S rRNA genes from bacteria and archaea in a sample followed by sequencing of the amplicons. The result is text files containing millions of short sequences. Those sequences are processed and analysed using a variety of tools. Those tools are often only able to perform parts of the analysis steps or require extensive knowledge and time to operate properly. During this project a processing and analysis pipeline for 16S rRNA amplicon data has been developed. It is able to take raw sequencing data, process it, analyse it and return an overview of the community structure. The program has been implemented on a server and can be accessed through a web interface where the user simply provides a email address and uploads the data, requiring no previous knowledge. The software has been compared to Qiime, one of the most widely used pipelines for amplicon sequencing analysis, showing that it is able to produce a similar taxonomic overview and estimates of the species richness and abundance. It is designed to be further extended, and is planned to be open sourced, allowing other programmers to contribute to its development in the future. In the moment of writing, the pipeline can be accessed through following temporary link: http: //130.235.244.91/Pipeline/.}}, author = {{Willforss, Jakob}}, language = {{eng}}, note = {{Student Paper}}, title = {{A rapid algorithm to describe community structure using next generation amplicon sequencing data}}, year = {{2015}}, }