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Compression of biological sequences
Šurín, Tomáš ; Mráz, František (advisor) ; Dvořák, Tomáš (referee)
Volumes of data obtained from the next generation sequencing platforms is growing faster than the available capacity of storage media. Sequencers mainly produce short reads of DNA. However, output of the sequencing machines also contains other information, for example information about read reliability/quality. This data must be archived even after successful complete genome assembly. Standard file format used for this type of data is format SAM (Sequence Alignment/Mapping Format) and its binary compressed version BAM. In this thesis we describe the construction of a better lossless compression scheme for compression of files in the SAM/BAM format. This compression scheme provides better compression ratios than the BAM format. In addition, random access to data in the compressed file is retained. Implementation of this compression scheme is platform independent and allows simple configuration of the compression process. Implementation also offers easy extensibility. Thanks to this, we will be able to respond to changes in current sequencing platforms as well as to changes in the SAM format.
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Wikipedia viewer for mobile devices
Šurín, Tomáš ; Žemlička, Michal (advisor) ; Kopecký, Michal (referee)
Unlimited access to encyclopedic or other reference sources of information is considered by many people to be very convenient. Thanks to various mobile devices with Internet access, this is possible nowadays. There are, however, situations when there is no available Internet connection or the users are not willing to pay for it. Be-cause of this we decided to allow offline access to this kind of information to users of mobile devices. Specifically we are trying to provide data from encyclopedia Wikipedia. We have chosen this encyclopedia because it is very comprehensive, it has good quality content and its data is freely available. Wikipedia runs on MediaWiki system, which is used in hundreds of other online projects. Additionally many corporations are using MediaWiki to manage their internal knowledgebase. Hence our solution can also provide data from these projects. Solution was designed with simple extensibility in mind as we are planning to add support for other information sources.
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Compression of biological sequences
Šurín, Tomáš ; Mráz, František (advisor) ; Dvořák, Tomáš (referee)
Volumes of data obtained from the next generation sequencing platforms is growing faster than the available capacity of storage media. Sequencers mainly produce short reads of DNA. However, output of the sequencing machines also contains other information, for example information about read reliability/quality. This data must be archived even after successful complete genome assembly. Standard file format used for this type of data is format SAM (Sequence Alignment/Mapping Format) and its binary compressed version BAM. In this thesis we describe the construction of a better lossless compression scheme for compression of files in the SAM/BAM format. This compression scheme provides better compression ratios than the BAM format. In addition, random access to data in the compressed file is retained. Implementation of this compression scheme is platform independent and allows simple configuration of the compression process. Implementation also offers easy extensibility. Thanks to this, we will be able to respond to changes in current sequencing platforms as well as to changes in the SAM format.
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Wikipedia viewer for mobile devices
Šurín, Tomáš ; Žemlička, Michal (advisor) ; Kopecký, Michal (referee)
Unlimited access to encyclopedic or other reference sources of information is considered by many people to be very convenient. Thanks to various mobile devices with Internet access, this is possible nowadays. There are, however, situations when there is no available Internet connection or the users are not willing to pay for it. Be-cause of this we decided to allow offline access to this kind of information to users of mobile devices. Specifically we are trying to provide data from encyclopedia Wikipedia. We have chosen this encyclopedia because it is very comprehensive, it has good quality content and its data is freely available. Wikipedia runs on MediaWiki system, which is used in hundreds of other online projects. Additionally many corporations are using MediaWiki to manage their internal knowledgebase. Hence our solution can also provide data from these projects. Solution was designed with simple extensibility in mind as we are planning to add support for other information sources.
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