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Open Access Highly Accessed Research article

Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

Jialei Duan12, Chuan Xia1, Guangyao Zhao1, Jizeng Jia1* and Xiuying Kong1*

Author Affiliations

1 Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 South Street, Zhongguancun, Beijing 100081, People's Republic of China

2 College of Biology Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100094, People's Republic of China

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BMC Genomics 2012, 13:392  doi:10.1186/1471-2164-13-392

Published: 14 August 2012

Additional files

Additional file 1:

Figure S1. Effects of merging assemblies of different samples and scaffolding (shown as changed proportions).

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Additional file 2:

Table S1. Detailed statistics for each assembly step.

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This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Table S2. Detailed pairwise comparisons between the six assemblies.

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Additional file 4:

Table S3. Sequences from A, B and D subgenome used in the assessment of parameters used in the step of removing redundancy.

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Additional file 5:

Table S4. Statistics of reads mapping to the assembled EST datasets (TAGI and TAPUT).

Format: XLS Size: 26KB Download file

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