Giddings M C, Severin J, Westphall M, Wu J, Smith L M
Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Genome Res. 1998 Jun;8(6):644-65. doi: 10.1101/gr.8.6.644.
Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing, analysis, and base-calling. BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilation. Powerful scripting capabilities combined with modularity and multilane handling allow the user to customize BaseFinder to virtually any type of trace processing. We have developed an extensive set of data processing and analysis modules for use with the program in fluorescence-based sequencing. GelImager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently allowing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapsody. Work is ongoing to deploy the software on additional platforms, including Solaris, Linux, and MacOS. This software has been thoroughly tested and debugged in the analysis of >2 million bp of raw sequence data from human chromosome 19 region q13. Overall sequencing accuracy was measured using a significant subset of these data, consisting of approximately 600 sequences, by comparing the individual shotgun sequences against the final assembled contigs. Also, results are reported from experiments that analyzed the accuracy of the software and two other well-known base-calling programs for sequencing the M13mp18 vector sequence. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422]
介绍了用于基于荧光测序的凝胶图像分析和碱基识别的软件，该软件由两个主要程序BaseFinder和GelImager组成。BaseFinder是一个用于轨迹处理、分析和碱基识别的框架。BaseFinder具有高度可扩展性，无需重新编译即可添加轨迹分析和处理模块。强大的脚本功能与模块化和多泳道处理相结合，允许用户将BaseFinder定制为几乎任何类型的轨迹处理。我们已经开发了一套广泛的数据处理和分析模块，用于基于荧光测序的程序。GelImager是一个用于凝胶图像处理的框架。它可用于凝胶可视化、泳道重新追踪，并作为华盛顿大学Getlanes程序的前端。这些程序是使用跨平台开发环境设计的，目前允许它们在Windows NT、Windows 95、Openstep/Mach和Rhapsody中运行。正在进行将该软件部署到其他平台的工作，包括Solaris、Linux和MacOS。该软件在分析来自人类19号染色体q13区域的超过200万碱基对的原始序列数据时经过了全面测试和调试。通过将单个鸟枪法序列与最终组装的重叠群进行比较，使用这些数据的一个重要子集（约600个序列）测量了总体测序准确性。此外，还报告了分析该软件和其他两个著名的碱基识别程序对M13mp18载体序列进行测序准确性的实验结果。[本文所述的序列数据已提交到GenBank数据库，登录号为AF025422]
