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A de novo paired-end reads assembler. PERGA can generate large and accurate assemblies using the greedy-like prediction strategy to handle branches and errors to give much better extensions. By using look-ahead approach, PERGA distinguishes sequencing errors and repeats accurately and separates different copies of short repeats to make the extension much longer and more accurate. Moreover, instead of using single-end reads to construct contigs, PERGA uses paired-end reads in the first step and gives different priority to different read overlap thresholds ranging from Omax to Omin to resolve the gap and branch problem.

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Command line interface
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  • Xiao Zhu <zhuxiao.hit at gmail.com>


Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China

Funding source(s)

This work was partially supported by the National Nature Science Foundation of China (61173085, 61102149 and 11171086), the National High-Tech Research and Development Program (863) of China (2012AA020404, 2012AA02A602 and 2012AA02A604), the Hong Kong GRF (HKU 7111/12E, HKU 719709E and 719611E), the Shenzhen Basic Research Project (NO.JCYJ20120618143038947), and the Outstanding Researcher Award (102009124).

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