An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals.
An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals.
复制标题
一种对来自多个个体的重叠双端 RAD 读数进行本地从头组装的优化方法
DOI：
10.1098/rsos.171589
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发表时间：
2018-03
影响因子：
3.5
通讯作者：
Liu JX
中科院分区：
文献类型：
--
作者：
Li YL;Xue DX;Zhang BD;Liu JX
限制性内切位点相关DNA （RAD）测序是生态、进化和保护基因组学研究的革命性进展。然而，具有随机剪切末端的成对RAD reads的组装仍然具有挑战性，特别是对于具有高遗传方差的非模式物种。在这里，我们提出了一种高效的优化方法，使用流水线软件RADassembler，它充分利用来自多个个体的随机剪切末端成对的RAD读取来组装RAD contigs。RADassembler集成了在聚类阶段选择个体内部和个体之间最优不匹配数的算法，然后在装配阶段使用两步装配方法。RADassembler还使用数据缩减和并行化策略来提高效率。与其他工具相比，基于仿真和真实RAD数据集的装配结果都表明，RADassembler总能高质量地组装出适当数量的contigs，并且更多的读对被正确映射到组装的contigs上。该方法为处理生态、进化和保护研究中非模式物种随机剪切末端对端RAD reads组装的复杂性提供了最佳工具。RADassembler可从https://github.com/lyl8086/RADscripts获得。
Restriction site-associated DNA (RAD) sequencing is revolutionizing studies in ecological, evolutionary and conservation genomics. However, the assembly of paired-end RAD reads with random-sheared ends is still challenging, especially for non-model species with high genetic variance. Here, we present an efficient optimized approach with a pipeline software, RADassembler, which makes full use of paired-end RAD reads with random-sheared ends from multiple individuals to assemble RAD contigs. RADassembler integrates the algorithms for choosing the optimal number of mismatches within and across individuals at the clustering stage, and then uses a two-step assembly approach at the assembly stage. RADassembler also uses data reduction and parallelization strategies to promote efficiency. Compared to other tools, both the assembly results based on simulation and real RAD datasets demonstrated that RADassembler could always assemble the appropriate number of contigs with high qualities, and more read pairs were properly mapped to the assembled contigs. This approach provides an optimal tool for dealing with the complexity in the assembly of paired-end RAD reads with random-sheared ends for non-model species in ecological, evolutionary and conservation studies. RADassembler is available at https://github.com/lyl8086/RADscripts.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
2.7
作者：
Harvey MG;Judy CD;Seeholzer GF;Maley JM;Graves GR;Brumfield RT
通讯作者：
Brumfield RT
影响因子：
3.7
作者：
Baxter SW;Davey JW;Johnston JS;Shelton AM;Heckel DG;Jiggins CD;Blaxter ML
通讯作者：
Blaxter ML
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
7
作者：
Miller, Michael R.;Dunham, Joseph P.;Johnson, Eric A.
通讯作者：
Johnson, Eric A.