Advanced

A rapid algorithm to describe community structure using next generation amplicon sequencing data

Willforss, Jakob LU (2015) KBK820 20151
Pure 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:
author
Willforss, Jakob LU
supervisor
organization
course
KBK820 20151
year
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},
  keyword      = {amplicon sequencing,pipeline},
  language     = {eng},
  note         = {Student Paper},
  title        = {A rapid algorithm to describe community structure using next generation amplicon sequencing data},
  year         = {2015},
}