Yuxuan Yuan1, Philipp E Bayer1, Huey-Tyng Lee1,2, David Edwards1. 1. School of Biological Sciences, University of Western Australia, Perth, WA, Australia. 2. School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.
Abstract
SUMMARY: We developed runBNG, an open-source software package which wraps BioNano genomic analysis tools into a single script that can be run on the command line. runBNG can complete analyses, including quality control of single molecule maps, optical map de novo assembly, comparisons between different optical maps, super-scaffolding and structural variation detection. Compared to existing software BioNano IrysView and the KSU scripts, the major advantages of runBNG are that the whole pipeline runs on one single platform and it has a high customizability. AVAILABILITY AND IMPLEMENTATION: runBNG is written in bash, with the requirement of BioNano IrysSolve packages, GCC, Perl and Python software. It is freely available at https://github.com/appliedbioinformatics/runBNG. CONTACT: dave.edwards@uwa.edu.au. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: We developed runBNG, an open-source software package which wraps BioNano genomic analysis tools into a single script that can be run on the command line. runBNG can complete analyses, including quality control of single molecule maps, optical map de novo assembly, comparisons between different optical maps, super-scaffolding and structural variation detection. Compared to existing software BioNano IrysView and the KSU scripts, the major advantages of runBNG are that the whole pipeline runs on one single platform and it has a high customizability. AVAILABILITY AND IMPLEMENTATION: runBNG is written in bash, with the requirement of BioNano IrysSolve packages, GCC, Perl and Python software. It is freely available at https://github.com/appliedbioinformatics/runBNG. CONTACT: dave.edwards@uwa.edu.au. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Yuxuan Yuan; Zbyněk Milec; Philipp E Bayer; Jan Vrána; Jaroslav Doležel; David Edwards; William Erskine; Parwinder Kaur Journal: Front Plant Sci Date: 2018-07-17 Impact factor: 5.753