SRComp : short read sequence compression using burstsort and Elias omega coding
Next-generation sequencing (NGS) technologies permit the rapid production of vast amounts of data at low cost. Economical data storage and transmission hence becomes an increasingly important challenge for NGS experiments. In this paper, we introduce a new non-reference based read sequence compres...
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| Main Authors: | , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
2013
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/99194 http://hdl.handle.net/10220/18351 |
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| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | Next-generation sequencing (NGS) technologies permit the rapid production of vast amounts of data at
low cost. Economical data storage and transmission hence becomes an increasingly important challenge
for NGS experiments. In this paper, we introduce a new non-reference based read sequence compression
tool called SRComp. It works by first employing a fast string-sorting algorithm called burstsort to sort
read sequences in lexicographical order and then Elias omega-based integer coding to encode the sorted
read sequences. SRComp has been benchmarked on four large NGS datasets, where experimental results
show that it can run 5-35 times faster than current state-of-the-art read sequence compression tools such
as BEETL and SCALCE, while retaining comparable compression efficiency for large collections of short
read sequences. SRComp is a read sequence compression tool that is particularly valuable in certain
applications where compression time is of major concern. |
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