A machine-readable specification for genomics assays

IF 4.4 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Bioinformatics Pub Date : 2024-04-01 DOI:10.1093/bioinformatics/btae168

A. S. Booeshaghi, Xi Chen, L. Pachter

引用次数: 0

Abstract

Abstract Motivation Understanding the structure of sequenced fragments from genomics libraries is essential for accurate read preprocessing. Currently, different assays and sequencing technologies require custom scripts and programs that do not leverage the common structure of sequence elements present in genomics libraries. Results We present seqspec, a machine-readable specification for libraries produced by genomics assays that facilitates standardization of preprocessing and enables tracking and comparison of genomics assays. Availability and implementation The specification and associated seqspec command line tool is available at https://www.doi.org/10.5281/zenodo.10213865.

查看原文本刊更多论文

基因组学测定的机器可读规范

摘要研究动机了解基因组文库中测序片段的结构对于准确进行读取预处理至关重要。目前，不同的检测方法和测序技术需要定制脚本和程序，而这些脚本和程序无法利用基因组文库中序列元素的共同结构。结果我们介绍了seqspec，这是一种针对基因组学检测产生的文库的机器可读规范，有助于预处理的标准化，并能对基因组学检测进行跟踪和比较。可用性和实施该规范和相关的 seqspec 命令行工具可在 https://www.doi.org/10.5281/zenodo.10213865 上获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Bioinformatics 生物-生化研究方法

CiteScore

11.20

自引率

5.20%

发文量

753

审稿时长

2.1 months

期刊介绍： The leading journal in its field, Bioinformatics publishes the highest quality scientific papers and review articles of interest to academic and industrial researchers. Its main focus is on new developments in genome bioinformatics and computational biology. Two distinct sections within the journal - Discovery Notes and Application Notes- focus on shorter papers; the former reporting biologically interesting discoveries using computational methods, the latter exploring the applications used for experiments.