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

English version

Autoři: Juhana I. Kammonen ^aff001; Olli-Pekka Smolander ^aff001; Lars Paulin ^aff001; Pedro A. B. Pereira ^aff001; Pia Laine ^aff001; Patrik Koskinen ^aff001; Jukka Jernvall ^aff003; Petri Auvinen ^aff001
Působiště autorů: DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland ^aff001; Department of Neurology, Helsinki University Hospital, Helsinki, Finland ^aff002; Evolutionary Phenomics Group, Institute of Biotechnology, University of Helsinki, Helsinki, Finland ^aff003
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0216885

Souhrn

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.

Klíčová slova:

Biology and life sciences – Genetics – Genomics – Genome analysis – Organisms – Eukaryota – Computational biology – Research and analysis methods – Sequence assembly tools – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – Animals – Microbiology – Vertebrates – Amniotes – Mammals – Genomic libraries – Bacteriology – Microbial genomics – BLAST algorithm – Computational techniques – Computational pipelines – Bacterial genetics – Bacterial genomics – Microbial genetics – Genomics statistics

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

Souhrn

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