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Full-Text Articles in Bioinformatics
Bpwrapper: Bioperl-Based Sequence And Tree Utilities For Rapid Prototyping Of Bioinformatics Pipelines, Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William Mccaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Weigang Qiu
Bpwrapper: Bioperl-Based Sequence And Tree Utilities For Rapid Prototyping Of Bioinformatics Pipelines, Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William Mccaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Weigang Qiu
Publications and Research
Abstract:
Background: Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl (http://bioperl.org) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users.
Results: Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of some of …