BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens

Mitchell Holland; Daniel Negrón; Shane Mitchell; Nate Dellinger; Mychal Ivancich; Tyler Barrus; Sterling Thomas; Katharine W. Jennings; Bruce Goodwin; Shanmuga Sozhamannan

The BioLaboro application is composed of a fully functional GUI front-end that allows 467 users to submit jobs to the back-end bioinformatics pipeline hosted on a dedicated large RAM 468 system. The system has multi-user capability with discrete logins and a single job queue. The The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 The BioLaboro application allows job submissions through a simplified user interface 475 designed for scientists with minimal or no command-line experience. The user can search for 476 sequences of interest using the built-in Organism Select tool, Figure 5 , which allows for 477 searching on free text, NCBI Accession number, or NCBI Taxonomy ID. The results can then be 478 filtered using a "smart filter" which will only include sequences within +/-10% of the calculated 479 median genome length of the results. This tool is useful for automatically excluding plasmids or 480 sequence fragments which can negatively impact signature identification. Alternatively, custom 481 sequence size filters can also be used if the user wants to target specific plasmids or 482 chromosomes. Once all sequences are selected and added the user can optionally choose a 483 specific sequence to serve as the algorithmic reference. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.031963 doi: bioRxiv preprint BioLaboro employs a queuing system to manage job submissions due to the high computational The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.08.031963 doi: bioRxiv preprint