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bioRxiv · 10.1101/2020.10.20.348052

orfipy: a fast and flexible tool for extracting ORFs

Singh, U.·Wurtele, E. S.
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Abstract

SummarySearching for ORFs in transcripts is a critical step prior to annotating coding regions in newly-sequenced genomes and to search for alternative reading frames within known genes. With the tremendous increase in RNA-Seq data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in fasta sequences. The search is rapid and is fully customizable, with a choice of Fasta and BED output formats. Availability and implementationorfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https://github.com/urmi-21/orfipy. Installation: from the source, or via PyPi (https://pypi.org/project/orfipy) or bioconda (https://anaconda.org/bioconda/orfipy). Contactusingh@iastate.edu, mash@iastate.edu Supplementary informationSupplementary data are available at https://github.com/urmi-21/orfipy

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Singh, U., Wurtele, E. S.. 2020-10-21. orfipy: a fast and flexible tool for extracting ORFs. https://doi.org/10.1101/2020.10.20.348052

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