title: ÐÐ¾Ð²ÑÑÐµÐ½Ð¸Ðµ Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´Ð¸ÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ñ Ð¼ÐµÑÑÐ¸ÐºÐ¸ CollectWGS Ð¿Ð°ÐºÐµÑÐ¾Ð¼ Picard Tools
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Improving the performance of calculating the CollectWGS metric by Picard Tools
Creators: name: ÐÐ°Ð¹ÑÐµÐ½ÐºÐ¾Ð², ÐÐ»ÐµÐºÑÐµÐ¹
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2020
Subjects: it-ÑÐµÑ Ð½Ð¾Ð»Ð¾Ð³Ð¸Ð¸
Ð³ÐµÐ½Ð¾Ð¼
Ð¼Ð½Ð¾Ð³Ð¾Ð¿Ð¾ÑÐ¾ÑÐ½Ð¾ÑÑÑ
Ð¿Ð¾Ð²ÑÑÐµÐ½Ð¸Ðµ Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´Ð¸ÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ñ
ÑÐ°ÑÐ¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ð½ÑÐµ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ñ
Ð¼ÐµÑÑÐ¸ÐºÐ¸ Ð³ÐµÐ½Ð¾Ð¼Ð°
picard tools
java
it-technologies
genome
multithreading
increasing calculation performance
distributed computing
genome metrics

description: Picard Tools â Ð½Ð°Ð±Ð¾Ñ ÑÑÐ¸Ð»Ð¸Ñ ÐºÐ¾Ð¼Ð°Ð½Ð´Ð½Ð¾Ð¹ ÑÑÑÐ¾ÐºÐ¸ Ð´Ð»Ñ ÑÐ°Ð±Ð¾ÑÑ Ñ ÑÐ°Ð¹Ð»Ð°Ð¼Ð¸ Ð³ÐµÐ½Ð¾Ð¼Ð½ÑÑ Ð¿Ð¾ÑÐ»ÐµÐ´Ð¾Ð²Ð°ÑÐµÐ»ÑÐ½Ð¾ÑÑÐµÐ¹. ÐÐ½ Ð¿ÑÐµÐ´Ð¾ÑÑÐ°Ð²Ð»ÑÐµÑ Ð¸Ð½ÑÑÑÑÐ¼ÐµÐ½ÑÑ Ð´Ð»Ñ Ð¸Ñ Ð¾Ð±ÑÐ°Ð±Ð¾ÑÐºÐ¸, Ð°Ð½Ð°Ð»Ð¸Ð·Ð° Ð¸ Ð²ÑÐ²Ð¾Ð´Ð° ÐµÐ³Ð¾ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐ¾Ð² Ð² Ð²Ð¸Ð´Ðµ ÑÐ°Ð·Ð»Ð¸ÑÐ½ÑÑ Ð¼ÐµÑÑÐ¸Ðº. CollectWGSMetrics Ð¸ÑÐ¿Ð¾Ð»ÑÐ·ÑÐµÑÑÑ Ð´Ð»Ñ Ð¾ÑÐµÐ½ÐºÐ¸ ÑÐµÐ·ÑÐ»ÑÑÐ°ÑÐ¾Ð² ÑÐ°Ð½ÐµÐµ Ð¿ÑÐ¾Ð¸Ð·Ð²ÐµÐ´ÐµÐ½Ð½Ð¾Ð¹ Ð¾Ð±ÑÐ°Ð±Ð¾ÑÐºÐ¸ Ð´Ð°Ð½Ð½ÑÑ â Ð¿ÑÐ¾ÑÐµÐ½ÑÐ° ÑÐ°Ð½ÐµÐµ Ð²ÑÑÐ¾Ð²Ð½ÐµÐ½Ð½ÑÑ Ð½Ð° Ð³ÐµÐ½Ð¾Ð¼ ÑÐ¸Ð´Ð¾Ð², Ð¿ÑÐ¾ÑÐµÐ´ÑÐ¸Ñ Ð±Ð°Ð·Ð¾Ð²ÑÐµ ÑÐ¸Ð»ÑÑÑÑ ÐºÐ°ÑÐµÑÑÐ²Ð°. Ð¢Ð°ÐºÐ¸Ð¼ Ð¾Ð±ÑÐ°Ð·Ð¾Ð¼ Ð¾Ð½Ð° Ð¿Ð¾Ð·Ð²Ð¾Ð»ÑÐµÑ ÐºÐ¾Ð½ÑÑÐ¾Ð»Ð¸ÑÐ¾Ð²Ð°ÑÑ ÐºÐ°ÑÐµÑÑÐ²Ð¾ Ð´ÑÑÐ³Ð¸Ñ ÑÐºÑÐ¿ÐµÑÐ¸Ð¼ÐµÐ½ÑÐ¾Ð². Ð Ð´Ð°Ð½Ð½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÐµ Ð¾Ð¿Ð¸ÑÐ°Ð½ Ð¿ÑÐ¾ÑÐµÑÑ Ð¿Ð¾Ð¸ÑÐºÐ° Ð¿ÑÑÐµÐ¹ Ð¿Ð¾Ð²ÑÑÐµÐ½Ð¸Ñ Ð¿ÑÐ¾Ð¸Ð·Ð²Ð¾Ð´Ð¸ÑÐµÐ»ÑÐ½Ð¾ÑÑÐ¸ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ñ ÑÑÐ¾Ð¹ Ð¼ÐµÑÑÐ¸ÐºÐ¸ Ð¸ ÑÐ°Ð·ÑÐ°Ð±Ð¾ÑÐºÐ¸ Ð¿ÑÐ¸Ð¼ÐµÐ½Ð¸Ð¼ÑÑ Ð´Ð»Ñ ÑÑÐ¾Ð³Ð¾ Ð°Ð»Ð³Ð¾ÑÐ¸ÑÐ¼Ð¾Ð². ÐÑÐ¸Ð²ÐµÐ´ÐµÐ½Ð¾ Ð²ÑÐµÐ¼Ñ ÑÐ°Ð±Ð¾ÑÑ Ð¿ÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ñ Ñ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð¸ÐµÐ¼ ÑÐ°Ð·Ð»Ð¸ÑÐ½ÑÑ Ð¿Ð¾Ð´ÑÐ¾Ð´Ð¾Ð² Ðº ÑÐµÑÐµÐ½Ð¸Ñ Ð·Ð°Ð´Ð°ÑÐ¸, Ð¿ÑÐ¾Ð°Ð½Ð°Ð»Ð¸Ð·Ð¸ÑÐ¾Ð²Ð°Ð½Ñ Ð´Ð°Ð½Ð½ÑÐµ, Ð¿Ð¾Ð»ÑÑÐµÐ½Ð½ÑÐµ Ð¸Ð· Ð»Ð¾Ð³Ð¾Ð² Ð¸ Ð¿ÑÐ¾ÑÐ¸Ð»Ð¸ÑÐ¾Ð²ÑÐ¸ÐºÐ¾Ð². Ð ÑÐ¾Ð´Ðµ Ð½ÐµÑ ÑÐ°ÑÑÐ¼Ð¾ÑÑÐµÐ½ Ð²Ð¾Ð¿ÑÐ¾Ñ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð¸Ñ ÑÐ°ÑÐ¿ÑÐµÐ´ÐµÐ»ÐµÐ½Ð½ÑÑ Ð¸ Ð¼Ð½Ð¾Ð³Ð¾Ð¿Ð¾ÑÐ¾ÑÐ½ÑÑ Ð²ÑÑÐ¸ÑÐ»ÐµÐ½Ð¸Ð¹ Ð´Ð»Ñ Ð±Ð¾Ð»ÐµÐµ ÑÑÑÐµÐºÑÐ¸Ð²Ð½Ð¾Ð³Ð¾ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð¸Ñ ÑÐµÑÑÑÑÐ¾Ð² Ð²ÑÑÐ¸ÑÐ»Ð¸ÑÐµÐ»ÑÐ½Ð¾Ð¹ ÑÐ¸ÑÑÐµÐ¼Ñ.
Ð Ð°Ð±Ð¾ÑÐ° Ð²ÐµÐ»Ð°ÑÑ Ð½Ð° ÑÐ·ÑÐºÐµ Java Ñ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð½Ð¸ÐµÐ¼ ÑÑÐ°Ð½Ð´Ð°ÑÑÐ½Ð¾Ð¹ Ð±Ð¸Ð±Ð»Ð¸Ð¾ÑÐµÐºÐ¸ Ð¸ Ð±Ð¸Ð±Ð»Ð¸Ð¾ÑÐµÐºÐ¸ htsjdk. ÐÐ¾ Ð¸ÑÐ¾Ð³Ð°Ð¼ ÑÐ°Ð±Ð¾ÑÑ ÑÐ°ÑÑÐ¸ÑÐµÐ½ ÑÑÐ½ÐºÑÐ¸Ð¾Ð½Ð°Ð» ÑÑÑÐµÑÑÐ²ÑÑÑÐµÐ³Ð¾ Ð¸Ð½ÑÑÑÑÐ¼ÐµÐ½ÑÐ° Ð¸ Ð¿ÑÐµÐ´Ð»Ð¾Ð¶ÐµÐ½Ñ Ð¿ÑÑÐ¸ Ð´Ð»Ñ ÐµÐ³Ð¾ Ð´Ð°Ð»ÑÐ½ÐµÐ¹ÑÐµÐ³Ð¾ ÑÑÐ¾Ð²ÐµÑÑÐµÐ½ÑÑÐ²Ð¾Ð²Ð°Ð½Ð¸Ñ.
description: Picard Tools is a set of command line utilities for working with genomic sequence files. It provides tools for their processing, analysis and output of its results in the form of various metrics.
CollectWGSMetrics is used to evaluate the results of previously performed data processing - the percentage of reads previously aligned to the genome that passed the basic quality filters. Thus, it allows you to control the quality of other experiments. This paper describes the process of finding ways to improve the performance of computing this metric and developing applicable algorithms for this. The operating time of the program using various approaches to solving the problem is given, data obtained from logs and profilers are analyzed. During it, the question of using distributed and multi-threaded computing for more efficient use of computer system resources was considered.
The work was conducted in the Java language using the standard library and the htsjdk library. Based on the results of the work, the functionality of the existing tool was expanded and ways for its further improvement were proposed.