Download
Share
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

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

, , , , , , ,
1 Institute of Biotechnology, University of Helsinki, Helsinki, Finland
2 Blueprint Genetics Ltd., Helsinki, Finland
DOI
10.7287/peerj.preprints.3467v1
Published
Accepted
Subject Areas
Bioinformatics, Genetics, Genomics, Computational Science
Keywords
scaffolding, draft genomes, genome assembly, next-generation sequencing, long read technologies
Copyright
© 2017 Kammonen et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Kammonen JI, Smolander O, Paulin L, Pereira PA, Laine P, Koskinen P, Jernvall J, Auvinen P. 2017. gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output. PeerJ Preprints 5:e3467v1

Abstract

Unknown sequences, or gaps, are largely present in most 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 many computational tools exist 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 software 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, but SSPACE-LongRead currently lacks this functionality. We present an automated pipeline called gapFinisher to process SSPACE-LongRead output to fill gaps after the actual scaffolding. gapFinisher is based on controlled use of a gap filling tool called FGAP and works on all standard Linux/UNIX command lines. We conclude that performing the workflows of SSPACE-LongRead and gapFinisher enables users to fill gaps reliably. There is no need for further scrutiny of the existing sequencing data after performing the analysis.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

minidot (Li, 2016) plots of the six bacterial genomes at different stages of the assembly

DOI: 10.7287/peerj.preprints.3467v1/supp-1

Mauve (Darling et al., 2004) alignments of the six bacterial genomes at different stages of the 10 assembly

DOI: 10.7287/peerj.preprints.3467v1/supp-2

All de novo assembly, scaffolding and gap filling statistics for the model genomes

DOI: 10.7287/peerj.preprints.3467v1/supp-3

Gap filling data used and FGAP (Piro et al., 2014) default test results reported for an unpublished draft genome of a marine mammal from the Phocidae family

DOI: 10.7287/peerj.preprints.3467v1/supp-4

Additional Information

Competing Interests

Patrik Koskinen currently is an employee of Blueprint Genetics Ltd. Finland. He was employed by the institution of the rest of the authors (Institute of Biotechnology, University of Helsinki) at the time when the actual work on this study started. The authors declare that they have no competing interests.

Author Contributions

Juhana I Kammonen conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Olli-Pekka Smolander performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Lars Paulin performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Pedro AB Pereira contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper, translation of FGAP program code from Portuguese to English.

Pia Laine performed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Patrik Koskinen conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Jukka Jernvall conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper, supervised the study as part of the PhD thesis of the first author..

Petri Auvinen conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, supervised the study as part of the PhD thesis of the first author..

Data Deposition

The following information was supplied regarding data availability:

1) University home page of the first author

2) Not available

3) http://www.helsinki.fi/~jkammone/gapFinisher.zip

Funding

This work was supported by the Jane and Aatos Erkko Foundation 2013 and 2017 (JJ & PA), as well as the Integrated Life Sciences Doctoral Programme (ILS), 2017-2018 (to JIK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies
Download
Content
Alert
Just enter your email

Download article

gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output
PDF Save to Mendeley RIS XML BibTeX
  Visitors   Views   Downloads