Naslov
EAGLER - Eliminating Assembly Gaps by Long Extending Reads

Autori
Šterbić, Luka

Vrsta, podvrsta i kategorija rada
Ocjenski radovi, diplomski rad, diplomski

Fakultet
Fakultet elektrotehnike i računarstva

Mjesto
Zagreb

Datum
01.12

Godina
2015

Stranica
57

Mentor
Šikić, Mile

Ključne riječi
Scaffolding; NGS; Long Reads; PacBio; Oxford Nanopore

Sažetak
Next Generation Sequencing (NGS) is rapidly becoming a cornerstone of clinical medicine. The limiting factor of NGS technologies is the inability to reconstruct genomic regions with high repeat rates since a single read can span only up to 300 base pairs. The EAGLER scaffolder is a post-assembly tool aimed at closing gaps in the draft assemblies created by NGS assemblers such as SGA, ABySS and SPAdes. The scaffolder takes as input a draft genome and a set of long reads, either PacBio or Nanopore, and outputs a set of scaffolds. It has shown very promising results on the Escherichia Coli K12 MG1655 genome achieving an average identity of 98.96% using PacBio long reads with a 20x coverage.

Izvorni jezik
Engleski

Znanstvena područja
Računarstvo

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