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Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)
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B. Gschloessl F. Dorkeld H. Berges G. Beydon O. Bouchez M. Branco A. Bretaudeau C. Burban E. Dubois P. Gauthier E. Lhuillier J. Nichols S. Nidelet S. Rocha L. Sauné R. Streiff M. Gautier C. Kerdelhué 《Molecular ecology resources》2018,18(3):602-619
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A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives
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Gautier Sarah Felix Homa Stéphanie Pointet Sandy Contreras François Sabot Benoit Nabholz Sylvain Santoni Laure Sauné Morgane Ardisson Nathalie Chantret Christopher Sauvage James Tregear Cyril Jourda David Pot Yves Vigouroux Hana Chair Nora Scarcelli Claire Billot Nabila Yahiaoui Roberto Bacilieri Bouchaib Khadari Michel Boccara Adéline Barnaud Jean‐Pierre Péros Jean‐Pierre Labouisse Jean‐Louis Pham Jacques David Sylvain Glémin Manuel Ruiz 《Molecular ecology resources》2017,17(3):565-580
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转录本组装是基于第二代测序技术研究转录组的关键环节,其质量好坏直接影响到下游结果的可靠性,也是目前的研究热点与难点。转录本组装方法可以分为Genome-guided和de novo两类,它们在理论基础与算法实现方面各有优劣。转录本组装质量的高低依赖于PCR扩增错误率、第二代测序技术准确率、组装算法和参考基因组完整性等方面,而现有的算法还无法完全处理由这些因素带来的影响。本文从转录本组装方法与软件、影响组装质量的因素和对组装质量的评价指标等方面进行讨论,以期能指导纯生物学家对分析软件的选择。 相似文献
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利用公共数据库中果蝇F1代和栽培水稻基于高通量Illumina测序平台的RNA Seq短序列数据,比较了8个 (ABySS, Velvet, SOAPdenovo, Oases, Trinity, Multiple k, T IDBA and Trans ABySS) 转录组从头组装软件。结果显示,在基于单一k mer和多重k mer方法的两类软件中,Trinity和Trans ABySS分别表现出最好的组装性能,而其它软件性能比较接近。我们还发现基于多重k mer比单一k mer可以组装获得更多的总碱基数目,但是即使利用最好的多重k mer组装软件,所获得的数据质量也比研究人员所期望的要低。鉴于此,我们提出了“ETM”优化方法,将多重k mer方法组合到Trinity中,使其在具有最好的组装性能的基础上兼具了多重k mer的优势,测试结果显示了该方法具有一定的优越性。我们的研究结果为用户选择合适的软件提供了依据,对推动基于高通量Illumina测序的转录组研究具有重要意义。 相似文献
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Rhys A. Farrer Eric Kemen Jonathan D.G. Jones & David J. Studholme 《FEMS microbiology letters》2009,291(1):103-111
Illumina's Genome Analyzer generates ultra-short sequence reads, typically 36 nucleotides in length, and is primarily intended for resequencing. We tested the potential of this technology for de novo sequence assembly on the 6 Mbp genome of Pseudomonas syringae pv. syringae B728a with several freely available assembly software packages. Using an unpaired data set, velvet assembled >96% of the genome into contigs with an N50 length of 8289 nucleotides and an error rate of 0.33%. edena generated smaller contigs (N50 was 4192 nucleotides) and comparable error rates. ssake and vcake yielded shorter contigs with very high error rates. Assembly of paired-end sequence data carrying 400 bp inserts produced longer contigs (N50 up to 15 628 nucleotides), but with increased error rates (0.5%). Contig length and error rate were very sensitive to the choice of parameter values. Noncoding RNA genes were poorly resolved in de novo assemblies, while >90% of the protein-coding genes were assembled with 100% accuracy over their full length. This study demonstrates that, in practice, de novo assembly of 36-nucleotide reads can generate reasonably accurate assemblies from about 40 × deep sequence data sets. These draft assemblies are useful for exploring an organism's proteomic potential, at a very economic low cost. 相似文献
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