PANDAseq: paired-end assembler for illumina sequences.
PANDAseq: paired-end assembler for illumina sequences.
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DOI：
10.1186/1471-2105-13-31
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发表时间：
2012-02-14
影响因子：
3
通讯作者：
Neufeld JD
中科院分区：
文献类型：
--
作者：
Masella AP;Bartram AK;Truszkowski JM;Brown DG;Neufeld JD
Illumina双端读段用于通过靶向16 S rRNA基因的扩增子来分析微生物群落。需要公开可用的工具来组装重叠的双端读段，同时纠正错配和未调用的碱基;可以使用质量信息纠正许多错误以获得更高的序列产率。PANDASeq快速组装双端读取，并纠正大多数错误。不确定的错误校正来自上游处理识别的具有许多低质量碱基的读段。使用真实的错误掩码对模拟数据、纯源模板和来自已知生物体的基因组DNA的合并模板进行基准测试。与替代方法相比，PANDASeq组装读数更快，错误掺入更少。PANDASeq快速组装序列，并扩展到数十亿个双端读取。对照文库的组装显示组装序列的数量比初始组装增加4-50%，“好”序列的损失可忽略不计。
Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods. PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.
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影响因子：
4.4
作者：
Bartram, Andrea K.;Lynch, Michael D. J.;Neufeld, Josh D.
通讯作者：
Neufeld, Josh D.
影响因子：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM
DOI：
10.1073/pnas.1000080107
发表时间：
2011-03-15
影响因子：
11.1
作者：
Caporaso, J. Gregory;Lauber, Christian L.;Knight, Rob
通讯作者：
Knight, Rob
影响因子：
14.9
作者：
Cock PJ;Fields CJ;Goto N;Heuer ML;Rice PM
通讯作者：
Rice PM
影响因子：
14.9
作者：
Cole JR;Chai B;Farris RJ;Wang Q;Kulam-Syed-Mohideen AS;McGarrell DM;Bandela AM;Cardenas E;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM