Wendl M C, Dear S, Hodgson D, Hillier L
Genome Sequencing Center, Washington University, St. Louis, Missouri 63108 USA.
Genome Res. 1998 Sep;8(9):975-84. doi: 10.1101/gr.8.9.975.
A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing of all trace data, including shotgun and finishing reads, regardless of clone origin. Design considerations are discussed in detail, as are programming implementation and graphic tools. The importance of input validation, record tracking, and use of base quality values is emphasized. Several quality analysis metrics are proposed and applied to sample results from recently sequenced clones. Such quantities prove to be a valuable aid in evaluating modifications of sequencing protocol. The system is in full production use at both the Genome Sequencing Center and the Sanger Centre, for which combined weekly production is approximately 100, 000 sequencing reads per week.
本文描述了一种软件系统，该系统可将基于四色荧光的凝胶电泳实验中的片段转化为组装序列。它是为大规模处理所有微量数据而开发的，包括鸟枪法测序和完成测序读段，无论克隆来源如何。详细讨论了设计考量、编程实现和图形工具。强调了输入验证、记录跟踪以及碱基质量值使用的重要性。提出了几种质量分析指标，并将其应用于最近测序克隆的样本结果。这些指标被证明是评估测序方案修改的宝贵辅助手段。该系统已在基因组测序中心和桑格中心全面投入生产使用，两者每周的联合产量约为每周100,000个测序读段。
