منابع مشابه
Compression of FASTQ and SAM Format Sequencing Data
Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both referenc...
متن کاملLFQC: a lossless compression algorithm for FASTQ files
MOTIVATION Next Generation Sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of l...
متن کاملCompression of DNA sequence reads in FASTQ format
MOTIVATION Modern sequencing instruments are able to generate at least hundreds of millions short reads of genomic data. Those huge volumes of data require effective means to store them, provide quick access to any record and enable fast decompression. RESULTS We present a specialized compression algorithm for genomic data in FASTQ format which dominates its competitor, G-SQZ, as is shown on ...
متن کاملManipulation of FASTQ data with Galaxy
SUMMARY Here, we describe a tool suite that functions on all of the commonly known FASTQ format variants and provides a pipeline for manipulating next generation sequencing data taken from a sequencing machine all the way through the quality filtering steps. AVAILABILITY AND IMPLEMENTATION This open-source toolset was implemented in Python and has been integrated into the online data analysis...
متن کاملTransformations for the compression of FASTQ quality scores of next-generation sequencing data
MOTIVATION The growth of next-generation sequencing means that more effective and efficient archiving methods are needed to store the generated data for public dissemination and in anticipation of more mature analytical methods later. This article examines methods for compressing the quality score component of the data to partly address this problem. RESULTS We compare several compression pol...
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ژورنال
عنوان ژورنال: Source Code for Biology and Medicine
سال: 2019
ISSN: 1751-0473
DOI: 10.1186/s13029-019-0073-5