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GTZ: a fast compression and cloud transmission tool optimized for FASTQ files

Overview of attention for article published in BMC Bioinformatics, December 2017
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About this Attention Score

  • Good Attention Score compared to outputs of the same age (70th percentile)
  • Good Attention Score compared to outputs of the same age and source (71st percentile)

Mentioned by

twitter
4 tweeters
patent
1 patent

Citations

dimensions_citation
8 Dimensions

Readers on

mendeley
19 Mendeley
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Title
GTZ: a fast compression and cloud transmission tool optimized for FASTQ files
Published in
BMC Bioinformatics, December 2017
DOI 10.1186/s12859-017-1973-5
Pubmed ID
Authors

Yuting Xing, Gen Li, Zhenguo Wang, Bolun Feng, Zhuo Song, Chengkun Wu

Abstract

The dramatic development of DNA sequencing technology is generating real big data, craving for more storage and bandwidth. To speed up data sharing and bring data to computing resource faster and cheaper, it is necessary to develop a compression tool than can support efficient compression and transmission of sequencing data onto the cloud storage. This paper presents GTZ, a compression and transmission tool, optimized for FASTQ files. As a reference-free lossless FASTQ compressor, GTZ treats different lines of FASTQ separately, utilizes adaptive context modelling to estimate their characteristic probabilities, and compresses data blocks with arithmetic coding. GTZ can also be used to compress multiple files or directories at once. Furthermore, as a tool to be used in the cloud computing era, it is capable of saving compressed data locally or transmitting data directly into cloud by choice. We evaluated the performance of GTZ on some diverse FASTQ benchmarks. Results show that in most cases, it outperforms many other tools in terms of the compression ratio, speed and stability. GTZ is a tool that enables efficient lossless FASTQ data compression and simultaneous data transmission onto to cloud. It emerges as a useful tool for NGS data storage and transmission in the cloud environment. GTZ is freely available online at: https://github.com/Genetalks/gtz .

Twitter Demographics

The data shown below were collected from the profiles of 4 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 19 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 21%
Student > Doctoral Student 3 16%
Researcher 3 16%
Professor > Associate Professor 2 11%
Student > Bachelor 2 11%
Other 1 5%
Unknown 4 21%
Readers by discipline Count As %
Computer Science 5 26%
Biochemistry, Genetics and Molecular Biology 3 16%
Agricultural and Biological Sciences 3 16%
Engineering 3 16%
Medicine and Dentistry 1 5%
Other 0 0%
Unknown 4 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 31 October 2019.
All research outputs
#4,268,551
of 16,110,746 outputs
Outputs from BMC Bioinformatics
#1,773
of 5,837 outputs
Outputs of similar age
#121,118
of 409,420 outputs
Outputs of similar age from BMC Bioinformatics
#126
of 446 outputs
Altmetric has tracked 16,110,746 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 5,837 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.1. This one has gotten more attention than average, scoring higher than 68% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 409,420 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 70% of its contemporaries.
We're also able to compare this research output to 446 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 71% of its contemporaries.