Abstract
Research in bioinformatics primarily involves collection and analysis of a large volume of genomic data. Naturally, it demands efficient storage and transfer of this huge amount of data. In recent years, some research has been done to find efficient compression algorithms to reduce the size of various sequencing data. One way to improve the transmission time of large files is to apply a maximum lossless compression on them. In this paper, we present SAMZIP, a specialized encoding scheme, for sequence alignment data in SAM (Sequence Alignment/Map) format, which improves the compression ratio of existing compression tools available. In order to achieve this, we exploit the prior knowledge of the file format and specifications. Our experimental results show that our encoding scheme improves compression ratio, thereby reducing overall transmission time significantly.
Highlights
One of the primary tasks in bioinformatics research is to collect and analyze large volume of genomic sequencing data
For the purpose of research, scientists and researchers need to transfer over the Internet large amount of alignment data represented in Sequence Alignment/Map (SAM) format
We present SAMZIP, an encoding scheme designed to work on SAM files, which improves compression ratio of the existing compression tools available
Summary
One of the primary tasks in bioinformatics research is to collect and analyze large volume of genomic sequencing data. Modern sequencing instruments are generating at least hundreds of millions of short reads. Along with novel sequencing technologies, many new alignment tools have evolved that can perform efficient read mapping against large reference sequences. Alignments generated from these tools have different formats, which is not helpful for downstream processing. In order to simplify this process, a common alignment format, such as Sequence Alignment/Map (SAM) has been designed. For the purpose of research, scientists and researchers need to transfer over the Internet large amount of alignment data represented in SAM format. Greater transmission delay has always been an obstacle in this process. One way to accomplish this goal is to apply a maximum lossless compression on the files to be transferred
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