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...
| Main Authors: | , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2013
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| Online Access: | https://hdl.handle.net/10356/99194 http://hdl.handle.net/10220/18351 |
| _version_ | 1811688165253054464 |
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| author | Selva, Jeremy John Chen, Xin |
| author2 | School of Physical and Mathematical Sciences |
| author_facet | School of Physical and Mathematical Sciences Selva, Jeremy John Chen, Xin |
| author_sort | Selva, Jeremy John |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T05:27:52Z |
| format | Journal Article |
| id | ntu-10356/99194 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:27:52Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | ntu-10356/991942023-02-28T19:30:36Z SRComp : short read sequence compression using burstsort and Elias omega coding Selva, Jeremy John Chen, Xin School of Physical and Mathematical Sciences DRNTU::Science::Physics 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. NMRC (Natl Medical Research Council, S’pore) Published version 2013-12-20T02:55:33Z 2019-12-06T20:04:23Z 2013-12-20T02:55:33Z 2019-12-06T20:04:23Z 2013 2013 Journal Article Selva, J. J., & Chen, X. (2013). SRComp : short read sequence compression using burstsort and Elias omega coding. PLoS ONE, 8(12), e81414-. 1932-6203 https://hdl.handle.net/10356/99194 http://hdl.handle.net/10220/18351 10.1371/journal.pone.0081414 24349065 174979 en PLoS ONE © 2013 Selva, Chen. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. application/pdf |
| spellingShingle | DRNTU::Science::Physics Selva, Jeremy John Chen, Xin SRComp : short read sequence compression using burstsort and Elias omega coding |
| title | SRComp : short read sequence compression using burstsort and Elias omega coding |
| title_full | SRComp : short read sequence compression using burstsort and Elias omega coding |
| title_fullStr | SRComp : short read sequence compression using burstsort and Elias omega coding |
| title_full_unstemmed | SRComp : short read sequence compression using burstsort and Elias omega coding |
| title_short | SRComp : short read sequence compression using burstsort and Elias omega coding |
| title_sort | srcomp short read sequence compression using burstsort and elias omega coding |
| topic | DRNTU::Science::Physics |
| url | https://hdl.handle.net/10356/99194 http://hdl.handle.net/10220/18351 |
| work_keys_str_mv | AT selvajeremyjohn srcompshortreadsequencecompressionusingburstsortandeliasomegacoding AT chenxin srcompshortreadsequencecompressionusingburstsortandeliasomegacoding |