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

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PREREQUISITE: A successful run of SSPACE-LongRead so that the directory "inner-scaffold-sequences" is created.

a. Installation

Get and install MATLAB Compiler runtime (MCR) from:

https://sourceforge.net/projects/fgap/files/MCR_LINUX64b.tar.gz

Follow the MCR installation instructions at:

https://github.com/pirovc/fgap

at chapters

"Download MCR" and "Install MCR".

FGAP itself is provided with the gapFinisher download so that does not need to be installed.

In your preferred installation directory (e.g. /usr/bin/ ; /home/user/bin/ ):

cd gapFinisher
chmod -R 775 *

NOTE: sudo the chmod if needed

b. Running gapFinisher

After steps in a.

./gapFinisher -i <PATH_TO_SSPACE_LONGREAD_OUTPUT_FOLDER> -l <PATH_TO_LONG_READS_FASTA_USED_WITH_SSPACE> -m <MCR_LOCATION> -t <NUM_THREADS>

Example:

./gapFinisher -i /home/kammoji/test/scaffolding/PacBio_scaffolder_results -l /home/kammoji/test/filtered_subreads.60X.fasta -m /home/kammoji/bin/MCR_LINUX64b/v717 -t 1
#NOTE: -t needs to be specified always! The current version of gapFinisher does not have a default set.

c. Contributors

Since version 0.1, following people have contributed to gapFinisher:

• Juhana I Kammonen
• Olli-Pekka Smolander
• Ari Löytynoja
• Pia K Laine
• Lars Paulin
• Pedro AB Pereira
• Patrik Koskinen
• Jukka Jernvall
• Petri Auvinen
• Carolin Kolmeder
• Tarja Sundell

d. Disclaimer

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version. Please see file "LICENSE" for details.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>

e. How to cite gapFinisher

Where applicable, please cite gapFinisher as:

Kammonen, JI, Smolander, OP., Paulin, L., Laine, P., Pereira, PAB., Koskinen, P., Jernvall J. & Auvinen, P. (2019). gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output. PLoS ONE 14(9): e0216885.