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Mycotools: An Automated and Scalable Platform for Comparative Genomics

Konkel, Z.; Slot, J.

2023-09-12 genomics
10.1101/2023.09.08.556886 bioRxiv
Show abstract

Comparative genomics comprises analyses that investigate the genetic basis of organismal biology and ecology, which have also been applied to high throughput trait screening for applied purposes. The number of fungal genomes deposited in publicly available databases are currently in exponential growth. Due to the limited cutting-edge software availability and size or efficiency constraints of web-based analyses, comparative genomics research is often conducted on local computing environments. There is thus a need for an efficient standardized framework for locally assimilating, curating, and interfacing with genomic data. We present Mycotools as a comparative genomics database software suite that automatically curates, updates, and standardizes local comparative genomics. Mycotools incorporates novel analysis pipelines that are built on a suite of modules that streamline routine-to-complex comparative genomic tasks. The Mycotools software suite serves as a foundation for accessible and reproducible large-scale comparative genomics on local compute systems.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.