Complete genome sequence of Oenococcus oeni strain K19-3 isolated from grape must

Article Biochemical Research Methods

GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Pierre-Alain Chaumeil et al.

Summary: This study presents an updated version of GTDB-Tk that uses a divide-and-conquer approach to reduce memory requirements while minimizing classification impact.

BIOINFORMATICS (2022)

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Article Biochemistry & Molecular Biology

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

Wenjun Li et al.

Summary: The RefSeq project at NCBI contains a vast number of bacterial and archaeal genomes and proteins, with a focus on reducing spurious annotation through the use of expanded protein family models. The Protein Family Models Entrez database provides users with access to the PFMs, supporting multi-genome analyses and connections to the literature. The reference and representative genome set of prokaryotic genomes within RefSeq is regularly recalculated and available for download and BLAST searches.

NUCLEIC ACIDS RESEARCH (2021)

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Article Biotechnology & Applied Microbiology

A graphical, interactive and GPU-enabled workflow to process long-read sequencing data

Shishir Reddy et al.

Summary: The lack of graphical bioinformatics tools and the challenge of configuring high performance software using GPUs have hindered the democratization of long-read sequencing technology. This study introduces a cloud-enabled workflow for analyzing nanopore sequencing data with interactive features and GPU support. The software tools demonstrated significant speedup and cost reduction in analyzing blood cancer cell line data, showcasing the potential for faster and more cost-effective cancer diagnostics using long-read sequencing technology.

BMC GENOMICS (2021)

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Article Biotechnology & Applied Microbiology