Dedhia N N, McCombie W R
Lita Annenberg Hazen Genome Sequencing Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Genome Res. 1998 Mar;8(3):313-8. doi: 10.1101/gr.8.3.313.
Tracking data flow in high throughput sequencing is important in maintaining a consistent number of successfully sequenced samples, making decisions on scheduling the flow of sequencing steps, resolving problems at various steps and tracking the status of different projects. This is especially critical when the laboratory is handling a multitude of projects. We have built a Web-based data flow tracking package, called Kaleidaseq, which allows us to monitor the flow and quality of sequencing samples through the steps of preparation of library plates, plaque-picking, preparation of templates, conducting sequencing reactions, loading of samples on gels, base-calling the traces, and calculating the quality of the sequenced samples. Kaleidaseq's suite of displays allows for outstanding monitoring of the production sequencing process. The online display of current information that Kaleidaseq provides on both project status and process queues sorted by project enables accurate real-time assessment of the necessary samples that must be processed to complete the project. This information allows the process manager to allocate future resources optimally and schedule tasks according to scientific priorities. Quality of the sequenced samples can be tracked on a daily basis, which allows the sequencing laboratory to maintain a steady performance level and quickly resolve dips in quality. Kaleidaseq has a simple easy-to-use interface that allows access to all major functions and process queues from one Web page. This software package is modular and designed to allow additional processing steps and new monitoring variables to be added and tracked with ease. Access to the underlying relational database is through the Perl DBI interface, which allows for the use of different relational databases. Kaleidaseq is available for free use by the academic community from http://www.cshl.org/kaleidaseq.
在高通量测序中追踪数据流对于维持成功测序样本数量的一致性、决定测序步骤的流程安排、解决各个步骤中的问题以及追踪不同项目的状态至关重要。当实验室处理众多项目时，这一点尤为关键。我们构建了一个名为Kaleidaseq的基于网络的数据流追踪软件包，它使我们能够通过文库板制备、菌斑挑选、模板制备、进行测序反应、将样本加载到凝胶上、对测序峰进行碱基识别以及计算测序样本质量等步骤来监测测序样本的流程和质量。Kaleidaseq的一系列显示功能能够出色地监测生产测序过程。Kaleidaseq提供的关于项目状态和按项目排序的流程队列的当前信息在线显示，使得能够对完成项目所需处理的必要样本进行准确的实时评估。这些信息使流程管理者能够优化分配未来资源，并根据科学优先级安排任务。可以每天追踪测序样本的质量，这使测序实验室能够保持稳定的性能水平，并迅速解决质量下降的问题。Kaleidaseq具有简单易用的界面，可从一个网页访问所有主要功能和流程队列。这个软件包是模块化的，设计用于轻松添加和追踪额外的处理步骤及新的监测变量。通过Perl DBI接口可访问底层关系数据库，这允许使用不同的关系数据库。学术界可从http://www.cshl.org/kaleidaseq免费使用Kaleidaseq。
