gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
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
doi:
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:
Research and analysis methods – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – BLAST algorithm – Computational techniques – Computational pipelines – Biology and life sciences – Microbiology – Bacteriology – Bacterial genetics – Bacterial genomics – Microbial genomics – Genetics – Microbial genetics – Genomics – Genome analysis – Sequence assembly tools – Genomics statistics – Computational biology – Genomic libraries – Organisms – Eukaryota – Animals – Vertebrates – Amniotes – Mammals
Zdroje
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