Improving genome assemblies using multi-platform sequence data
12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2015, Naples, İtalya, 10 - 12 Eylül 2015, cilt.9874 LNCS, ss.220-232, (Tam Metin Bildiri)
- Yayın Türü: Bildiri / Tam Metin Bildiri
- Cilt numarası: 9874 LNCS
- Doi Numarası: 10.1007/978-3-319-44332-4_17
- Basıldığı Şehir: Naples
- Basıldığı Ülke: İtalya
- Sayfa Sayıları: ss.220-232
- Anahtar Kelimeler: Assembly improvement, de novo assembly, Next generation multi-platform sequencing
- Boğaziçi Üniversitesi Adresli: Evet
Özet
Accurate de novo assembly using short reads generated by next generation sequencing technologies is still an open problem. Although there are several assembly algorithms developed for data generated with different sequencing technologies, and some that can make use of hybrid data, the assemblies are still far from being perfect. There is still a need for computational approaches to improve draft assemblies. Here we propose a new method to correct assembly mistakes when there are multiple types of data generated using different sequencing technologies that have different strengths and biases. We exploit the assembly of highly accurate short reads to correct the contigs obtained from less accurate long reads. We apply our method to Illumina, 454, and Ion Torrent data, and also compare our results with existing hybrid assemblers, Celera and Masurca.