Editing Open reading frame (section)

=== orfipy ===
orfipy is a tool written in [[Python (programming language) |Python]] / [[Cython]] to extract ORFs in an extremely and fast and flexible manner.<ref>{{cite journal | vauthors = Singh U, Wurtele ES | title = orfipy: a fast and flexible tool for extracting ORFs | journal = Bioinformatics | date = February 2021 | volume = 37 | issue = 18 | pages = 3019–3020 | pmid = 33576786 | doi = 10.1093/bioinformatics/btab090| issn=1367-4803  | pmc = 8479652 | doi-access = free }}</ref> orfipy can work with plain or gzipped FASTA and FASTQ sequences, and provides several options to fine-tune ORF searches; these include specifying the start and stop codons, reporting partial ORFs, and using custom translation tables. The results can be saved in multiple formats, including the space-efficient BED format. orfipy is particularly faster for data containing multiple smaller FASTA sequences, such as de-novo transcriptome assemblies.<ref>{{Citation| vauthors = Singh U |title=urmi-21/orfipy|date=2021-02-13|url=https://github.com/urmi-21/orfipy|access-date=2021-02-13}}</ref>