Foundations for faster external sorting

1994 ◽  
pp. 414-425 ◽  
Author(s):  
Vladimir Estivill-Castro ◽  
Derick Wood
Keyword(s):  
External Sorting

External Sorting and Permuting

2008 ◽  
pp. 291-297
Author(s):  
Jeffrey Scott Vitter
Keyword(s):  
External Sorting

An external sorting algorithm

Cybernetics ◽  
1968 ◽  
Vol 2 (5) ◽  
pp. 75-79
Author(s):  
V. A. Litvinov
Keyword(s):  
Sorting Algorithm ◽  
External Sorting

External Sorting and Permuting

2015 ◽  
pp. 1-10
Author(s):  
Jeffrey Scott Vitter
Keyword(s):  
External Sorting

Parallel External Sorting

1985 ◽  
pp. 193-210
Author(s):  
SELIM G. AKL
Keyword(s):  
External Sorting

scholarly journals BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis

2020 ◽  
Vol 36 (9) ◽  
pp. 2705-2711 ◽  
Author(s):  
Gianvito Urgese ◽  
Emanuele Parisi ◽  
Orazio Scicolone ◽  
Santa Di Cataldo ◽  
Elisa Ficarra
Keyword(s):  
Sequence Analysis ◽  
Supplementary Information ◽  
Sorting Algorithm ◽  
Rna Seq ◽  
Compact Sets ◽  
Analysis Pipeline ◽  
Alignment Algorithms ◽  
External Sorting ◽  
Computational Resources ◽  
Generation Sequencing

Abstract Motivation High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially for machines with limited hardware capabilities. As the redundancy of the sequences typically increases with coverage, collapsing such files into compact sets of non-redundant reads has the 2-fold advantage of reducing file size and speeding-up the alignment, avoiding to map the same sequence multiple times. Method BioSeqZip generates compact and sorted lists of alignment-ready non-redundant sequences, keeping track of their occurrences in the raw files as well as of their quality score information. By exploiting a memory-constrained external sorting algorithm, it can be executed on either single- or multi-sample datasets even on computers with medium computational capabilities. On request, it can even re-expand the compacted files to their original state. Results Our extensive experiments on RNA-Seq data show that BioSeqZip considerably brings down the computational costs of a standard sequence analysis pipeline, with particular benefits for the alignment procedures that typically have the highest requirements in terms of memory and execution time. In our tests, BioSeqZip was able to compact 2.7 billion of reads into 963 million of unique tags reducing the size of sequence files up to 70% and speeding-up the alignment by 50% at least. Availability and implementation BioSeqZip is available at https://github.com/bioinformatics-polito/BioSeqZip. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Efficient External Sorting on Flash Memory Embedded Devices

2013 ◽  
Vol 5 (1) ◽  
pp. 1-20 ◽  
Author(s):  
Tyler Cossentine ◽  
Ramon Lawrence
Keyword(s):  
Flash Memory ◽  
Embedded Devices ◽  
External Sorting
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