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

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'gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output' https://t.co/jRTw3rAGIT
RT @kammoji: My preprint has been published today in @PeerJPreprints https://t.co/nfuUG4Gs6z #Bioinformatics #Genetics #Genomics #Computati…
216 days ago
gapFinisher: a reliable gap filling pipeline for SSPACE-LongRead scaffolder output https://t.co/3uvbNdd6Cq
My preprint has been published today in @PeerJPreprints https://t.co/nfuUG4Gs6z #Bioinformatics #Genetics #Genomics #ComputationalScience
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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Gap filling data used and FGAP (Piro et al., 2014) default test results reported for an unpublished draft genome of a marine mammal from the Phocidae family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.


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