Opfi : A Python package for identifying gene clusters in large genomics and metagenomics data sets
Gene clusters are sets of co-localized, often contiguous genes that together perform specific functions, many of which are relevant to biotechnology. There is a need for software tools that can extract candidate gene clusters from vast amounts of available genomic data. Therefore, we developed Opfi:...
| Veröffentlicht in: | Journal of open source software. - 2017. - 6(2021), 66 vom: 29. |
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| 1. Verfasser: | |
| Weitere Verfasser: | , , , |
| Format: | Online-Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2021
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| Zugriff auf das übergeordnete Werk: | Journal of open source software |
| Schlagworte: | Journal Article |
| Zusammenfassung: | Gene clusters are sets of co-localized, often contiguous genes that together perform specific functions, many of which are relevant to biotechnology. There is a need for software tools that can extract candidate gene clusters from vast amounts of available genomic data. Therefore, we developed Opfi: a modular pipeline for identification of arbitrary gene clusters in assembled genomic or metagenomic sequences. Opfi contains functions for annotation, de-deduplication, and visualization of putative gene clusters. It utilizes a customizable rule-based filtering approach for selection of candidate systems that adhere to user-defined criteria. Opfi is implemented in Python, and is available on the Python Package Index and on Bioconda (Grüning et al., 2018) |
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| Beschreibung: | Date Revised 28.03.2023 published: Print-Electronic Citation Status PubMed-not-MEDLINE |
| ISSN: | 2475-9066 |
| DOI: | 10.21105/joss.03678 |