Figaro: a novel statistical method for vector sequence removal
Figaro: a novel statistical method for vector sequence removal
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DOI：
10.1093/bioinformatics/btm632
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发表时间：
2008-02-15
期刊：
影响因子：
5.8
通讯作者：
Pop, Mihai
中科院分区：
文献类型：
--
作者：
White, James Robert;Roberts, Michael;Pop, Mihai
动机：自动桑格测序仪产生的序列末端常常包含克隆载体的片段。目前可用于识别和去除载体序列的软件工具需要了解载体序列、特定的剪接位点以及实验中使用的任何衔接子序列，而这些信息在公共数据库中经常被遗漏。此外，剪辑坐标本身缺失或报告有误。例如，在存入美国国家生物技术信息中心（NCBI）序列追踪档案库的12.4亿条鸟枪法测序序列中，多达7.35亿条（60%）缺乏载体剪辑信息。正确的剪辑信息对于试图验证、改进甚至完善大量以草图质量水平发布的基因组的科学家来说至关重要。
结果：我们在此介绍费加罗（Figaro），这是一种新型软件工具，可在事先不了解载体序列的情况下从原始序列数据中识别和去除载体。通过使用泊松统计分析短寡核苷酸的出现频率来自动推断载体序列。我们表明，在对来自拟暗果蝇的150万条鸟枪法测序读段进行测试时，费加罗达到了99.98%的灵敏度。我们通过重新组装存入序列追踪档案库的鸟枪法测序的两个细菌基因组，进一步探究了准确的载体修剪对全基因组组装质量的影响。费加罗被设计为大型计算流程中的一个模块，它快速、轻巧且灵活。
Motivation: Sequences produced by automated Sanger sequencing machines frequently contain fragments of the cloning vector on their ends. Software tools currently available for identifying and removing the vector sequence require knowledge of the vector sequence, specific splice sites and any adapter sequences used in the experimentinformation often omitted from public databases. Furthermore, the clipping coordinates themselves are missing or incorrectly reported. As an example, within the 1.24 billion shotgun sequences deposited in the NCBI Trace Archive, as many as 735 million (60) lack vector clipping information. Correct clipping information is essential to scientists attempting to validate, improve and even finish the increasingly large number of genomes released at a draft quality level.Results: We present here Figaro, a novel software tool for identifying and removing the vector from raw sequence data without prior knowledge of the vector sequence. The vector sequence is automatically inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics. We show that Figaro achieves 99.98 sensitivity when tested on 1.5 million shotgun reads from Drosophila pseudoobscura. We further explore the impact of accurate vector trimming on the quality of whole-genome assemblies by re-assembling two bacterial genomes from shotgun sequences deposited in the Trace Archive. Designed as a module in large computational pipelines, Figaro is fast, lightweight and flexible.