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PreprintCC BYbioRxiv

taxutils: Tools for managing and operating on NCBI taxonomy and accession mappings

  • W. O'Brien
  • S. Lee
  • V. Agarwal
  • E. Eskin1
  1. 1UCLA
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Abstract

Research in bioinformatics demands that many workflows and operations be consistently repeated across different tools. These operations include managing a taxdump, dealing with accession mappings, and performing analysis on the taxonomic tree. We introduce taxutils to address and alleviate the strain of these common workflows. To exhibit the extent of the package's capabilities, we introduce a strategy for assessing quality of an assembly via its potential impact on and perturbation of its mapping to a lowest-common-ancestor index. We illustrate the steps required for such an analysis, and show how the tool makes data management easy and otherwise-complex workflows simple.

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Cite

BibTeXRIS
BibTeX
@misc{obrien2026taxutils,
  title = {{taxutils: Tools for managing and operating on NCBI taxonomy and accession mappings}},
  author = {W. O'Brien and S. Lee and V. Agarwal and E. Eskin},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.18.752821},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.18.752821v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - taxutils: Tools for managing and operating on NCBI taxonomy and accession mappings
AU  - W. O'Brien
AU  - S. Lee
AU  - V. Agarwal
AU  - E. Eskin
PY  - 2026
DA  - 2026/09/18
PB  - bioRxiv
DO  - 10.64898/2026.09.18.752821
UR  - https://www.biorxiv.org/content/10.64898/2026.09.18.752821v1
AB  - Research in bioinformatics demands that many workflows and operations be consistently repeated across different tools. These operations include managing a taxdump, dealing with accession mappings, and performing analysis on the taxonomic tree. We introduce taxutils to address and alleviate the strain of these common workflows. To exhibit the extent of the package's capabilities, we introduce a strategy for assessing quality of an assembly via its potential impact on and perturbation of its mapping to a lowest-common-ancestor index. We illustrate the steps required for such an analysis, and show how the tool makes data management easy and otherwise-complex workflows simple.
ER  -