Reducing the number of artifactual repeats in de novo assembly of RNA-Seq data by optimizing the assembly pipeline

• Main Authors: Lee, Wei Kang, Mohd Zainuddin, Nur Afiza, Teh, Hui Ying, Lim, Yi Yi, Jaafar, Mohd Uzair, Khoo, Jia Shiun, Ghazali, Ahmad Kamal, Namasivayam, Parameswari, Abdullah, Janna Ong, Ho, Chai Ling
• Format: Article
• Language: English
• Published: Elsevier 2017
• Online Access: http://psasir.upm.edu.my/id/eprint/62927/1/Reducing%20the%20number%20of%20artifactual%20repeats%20in%20de%20novo%20.pdf; http://psasir.upm.edu.my/id/eprint/62927/; https://www.sciencedirect.com/science/article/pii/S2452014417300572

One of the problems of de novo assembly is the occurrence of artifactual direct or inverted repeats that are mainly formed by misassembly of short sequencing reads and cannot be differentiated from real sequence repeats. In this study, we compared the frequency of artifactual repeats generated by fo...