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. 2021 Oct 22;12:739054. doi: 10.3389/fgene.2021.739054

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Copyright © 2021 Balan, Jenkinson, Nair, Saha, Koganti, Voss, Zysk, Barr Fritcher, Ross, Giannini, Raghunathan, Kipp, Jenkins, Ida, Halling, Blackburn, Dasari, Oliver and Klee.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Pipeline completion time in minutes for the 4 tools. For Analysis 1, STAR-Fusion was the fastest among the 4 tools with median completion time of 6 min followed by Tophat Fusion at 20 min, SeekFusion at 45 min and JAFFA-Hybrid at 196 min. For Analysis 2, STAR-Fusion had a median completion time of 29 min, SeekFusion had a median completion time of 36 min, Tophat-Fusion had a median completion time of 53 min and JAFFA-Hybrid exhibited scalability issues withe pipeline failing due to memory issues after running for over 24 h (so the data was capped at 400 min for JAFFA Hybrid in the raw FASTQ mode). To circumvent the scalability issues, analysis in direct mode of JAFFA was performed and this mode demonstrated the fastest median completion time of 20 min.