gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output.

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ID: 58659
2019
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Abstract
Unknown sequences, or gaps, are present in many published genomes across public databases. Gap filling is an important finishing step in de novo genome assembly, especially in large genomes. The gap filling problem is nontrivial and while there are many computational tools partially solving the problem, several have shortcomings as to the reliability and correctness of the output, i.e. the gap filled draft genome. SSPACE-LongRead is a scaffolding tool that utilizes long reads from multiple third-generation sequencing platforms in finding links between contigs and combining them. The long reads potentially contain sequence information to fill the gaps created in the scaffolding, but SSPACE-LongRead currently lacks this functionality. We present an automated pipeline called gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. We compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. We conclude that gapFinisher can fill gaps in draft genomes quickly and reliably. In addition, the serial design of gapFinisher makes it scale well from prokaryote genomes to larger genomes with no increase in the computational footprint.
Reference Key
kammonen2019gapfinisherplos Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Kammonen, Juhana I;Smolander, Olli-Pekka;Paulin, Lars;Pereira, Pedro A B;Laine, Pia;Koskinen, Patrik;Jernvall, Jukka;Auvinen, Petri;
Journal PloS one
Year 2019
DOI
10.1371/journal.pone.0216885
URL
Keywords
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