开始使用命令行生物信息学的十条简单规则。 - Suppr

Ten simple rules for getting started with command-line bioinformatics.

作者信息

Brandies Parice A, Hogg Carolyn J

机构信息

School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia.

出版信息

PLoS Comput Biol. 2021 Feb 18;17(2):e1008645. doi: 10.1371/journal.pcbi.1008645. eCollection 2021 Feb.

DOI:10.1371/journal.pcbi.1008645

PMID:33600404

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7891784/

Abstract

摘要

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82e3/7891784/dea0fe1ab223/pcbi.1008645.g001.jpg

相似文献

Ten simple rules for getting started with command-line bioinformatics.开始使用命令行生物信息学的十条简单规则。

PLoS Comput Biol. 2021 Feb 18;17(2):e1008645. doi: 10.1371/journal.pcbi.1008645. eCollection 2021 Feb.

Genome Sequencing and Analysis Methods in Chronic Lymphocytic Leukemia.慢性淋巴细胞白血病中的基因组测序与分析方法

Methods Mol Biol. 2019;1881:319-325. doi: 10.1007/978-1-4939-8876-1_22.

Mingle: A Command Line Utility for Merging Multi-fasta Files.Mingle：一个用于合并多fasta文件的命令行实用工具。

J Comput Biol. 2019 Apr;26(4):396-404. doi: 10.1089/cmb.2018.0243. Epub 2019 Feb 14.

Whole-Genome Bisulfite Sequencing for the Methylation Analysis of Insect Genomes.用于昆虫基因组甲基化分析的全基因组亚硫酸氢盐测序

Methods Mol Biol. 2019;1858:141-156. doi: 10.1007/978-1-4939-8775-7_11.

DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.DeepVariant-on-Spark：使用基于云的计算框架进行小规模基因组分析。

Comput Math Methods Med. 2020 Sep 1;2020:7231205. doi: 10.1155/2020/7231205. eCollection 2020.

Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software.全面评估和特征分析短读通用结构变异调用软件。

Nat Commun. 2019 Jul 19;10(1):3240. doi: 10.1038/s41467-019-11146-4.

African swine fever whole-genome sequencing-Quantity wanted but quality needed.非洲猪瘟全基因组测序——数量很重要，但质量更关键。

PLoS Pathog. 2020 Aug 27;16(8):e1008779. doi: 10.1371/journal.ppat.1008779. eCollection 2020 Aug.

Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.利用短读长和链接读进行结构变异的综合分析可产生高度特异性和敏感性的预测结果。

PLoS Comput Biol. 2020 Nov 23;16(11):e1008397. doi: 10.1371/journal.pcbi.1008397. eCollection 2020 Nov.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data.MethylStar：一个快速且稳健的用于批量或单细胞全基因组 bisulfite 测序数据的预处理流水线。

BMC Genomics. 2020 Jul 13;21(1):479. doi: 10.1186/s12864-020-06886-3.

An introduction to high-throughput sequencing experiments: design and bioinformatics analysis.高通量测序实验介绍：设计与生物信息学分析

Methods Mol Biol. 2013;1038:1-26. doi: 10.1007/978-1-62703-514-9_1.

引用本文的文献

The changing landscape of text mining: a review of approaches for ecology and evolution.文本挖掘的变化格局：对生态学和进化学方法的综述。

Proc Biol Sci. 2024 Jul;291(2027):20240423. doi: 10.1098/rspb.2024.0423. Epub 2024 Jul 31.

The "Dry-Lab" Side of Food Authentication: Benchmark of Bioinformatic Pipelines for the Analysis of Metabarcoding Data.食品认证中的“干实验室”方面：用于代谢条形码数据分析的生物信息学流程基准

Foods. 2024 Jul 1;13(13):2102. doi: 10.3390/foods13132102.

A Bioinformatics Toolkit for Next-Generation Sequencing in Clinical Oncology.临床肿瘤学中用于下一代测序的生物信息学工具包。

Curr Issues Mol Biol. 2023 Dec 4;45(12):9737-9752. doi: 10.3390/cimb45120608.

Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework.监测环境微生物群落：在文化融合的课程与研究框架内整合微生物学与计算生物学能力。

Mol Ecol Resour. 2025 Feb;25(2):e13867. doi: 10.1111/1755-0998.13867. Epub 2023 Sep 13.

Ten simple rules for using public biological data for your research.使用公共生物数据进行研究的十个简单规则。

PLoS Comput Biol. 2023 Jan 5;19(1):e1010749. doi: 10.1371/journal.pcbi.1010749. eCollection 2023 Jan.

Ten simple rules for investigating (meta)genomic data from environmental ecosystems.从环境生态系统中研究（元）基因组数据的十条简单规则。

PLoS Comput Biol. 2022 Dec 8;18(12):e1010675. doi: 10.1371/journal.pcbi.1010675. eCollection 2022 Dec.

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.利用虚拟互动将高级学习融入生物信息学短期课程的十条简单规则。

PLoS Comput Biol. 2022 Jul 28;18(7):e1010220. doi: 10.1371/journal.pcbi.1010220. eCollection 2022 Jul.

Improving bioinformatics software quality through incorporation of software engineering practices.通过融入软件工程实践提高生物信息学软件质量。

PeerJ Comput Sci. 2022 Jan 5;8:e839. doi: 10.7717/peerj-cs.839. eCollection 2022.

FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.FA-nf：一种用Nextflow实现的针对非模式生物蛋白质的功能注释流程

Genes (Basel). 2021 Oct 19;12(10):1645. doi: 10.3390/genes12101645.

Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster.使用高性能计算（HPC）取得成功的十五个快速提示，即合理地操作那个Linux集群。

PLoS Comput Biol. 2021 Aug 5;17(8):e1009207. doi: 10.1371/journal.pcbi.1009207. eCollection 2021 Aug.

本文引用的文献

Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data.用于植物NGS数据分析的读段比对和变异检测工具比较

Plants (Basel). 2020 Apr 2;9(4):439. doi: 10.3390/plants9040439.

Ten simple rules for providing effective bioinformatics research support.提供有效生物信息学研究支持的十个简单规则。

PLoS Comput Biol. 2020 Mar 26;16(3):e1007531. doi: 10.1371/journal.pcbi.1007531. eCollection 2020 Mar.

Ten simple rules for documenting scientific software.记录科学软件的十条简单规则。

PLoS Comput Biol. 2018 Dec 20;14(12):e1006561. doi: 10.1371/journal.pcbi.1006561. eCollection 2018 Dec.

Bioconda: sustainable and comprehensive software distribution for the life sciences.生物conda：面向生命科学的可持续且全面的软件发行平台。

Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7.

Earth BioGenome Project: Sequencing life for the future of life.地球生物基因组计划：为生命的未来测序生命。

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333. doi: 10.1073/pnas.1720115115.

10KP: A phylodiverse genome sequencing plan.10KP：一个系统发育多样化的基因组测序计划。

Gigascience. 2018 Mar 1;7(3):1-9. doi: 10.1093/gigascience/giy013.

A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective.从头基因组组装软件的综合研究：当前挑战与未来展望

Evol Bioinform Online. 2018 Feb 20;14:1176934318758650. doi: 10.1177/1176934318758650. eCollection 2018.

Ten simple rules for biologists learning to program.生物学家学习编程的十条简单规则。

PLoS Comput Biol. 2018 Jan 4;14(1):e1005871. doi: 10.1371/journal.pcbi.1005871. eCollection 2018 Jan.

Evaluation and comparison of computational tools for RNA-seq isoform quantification.RNA测序异构体定量计算工具的评估与比较

BMC Genomics. 2017 Aug 7;18(1):583. doi: 10.1186/s12864-017-4002-1.

Advancing Genomics through the Global Invertebrate Genomics Alliance (GIGA).通过全球无脊椎动物基因组学联盟（GIGA）推动基因组学发展。

Invertebr Syst. 2017 Mar;31(1):1-7. doi: 10.1071/is16059. Epub 2017 Mar 16.

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

Ten simple rules for getting started with command-line bioinformatics.

作者信息

机构信息

出版信息

相似文献

引用本文的文献

本文引用的文献

文献检索

文件翻译

深度研究

Suppr 超能文献

相似文献

引用本文的文献

本文引用的文献