High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.
%0 Journal Article
%1 leipzig2017review
%A Leipzig, J
%D 2017
%J Brief Bioinform
%K pipeline
%N 3
%P 530-536
%R 10.1093/bib/bbw020
%T A review of bioinformatic pipeline frameworks
%U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429012/
%V 18
%X High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.
@article{leipzig2017review,
abstract = {High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of several current pipeline frameworks. I provide practical recommendations based on analysis requirements and the user base.},
added-at = {2018-07-25T06:35:47.000+0200},
author = {Leipzig, J},
biburl = {https://www.bibsonomy.org/bibtex/22fd7189189001a00077f00f41310319e/robin.garcia},
description = {A review of bioinformatic pipeline frameworks},
doi = {10.1093/bib/bbw020},
interhash = {e8ed059eaba5462c762281a2f55c1050},
intrahash = {2fd7189189001a00077f00f41310319e},
journal = {Brief Bioinform},
keywords = {pipeline},
month = {05},
number = 3,
pages = {530-536},
pmid = {27013646},
timestamp = {2018-07-25T06:35:47.000+0200},
title = {A review of bioinformatic pipeline frameworks},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429012/},
volume = 18,
year = 2017
}