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The command-line implementation of NAST was used in this study, and compared directly with command-line PyNAST.
Command line script execution can be initiated using the standard Perl command line syntax of "perl Prep.pl Keywords".
These command line utilities serve as reference implementations of the routines implemented in the library and can readily be used for atomic tasks in NGS data processing.
It is a flexible framework that allows the implementation of command line driver scripts (in the form of Python object classes) that can be customized easily by overriding specific object methods.
In order to simplify the development and implementation task, already existing command line tools were selected to carry out all interaction with the used storage services.
We first provide a conceptional overview of the implementation of the chemalot command line programs by describing three representative programs and the KNIME framework for the dynamic node generation.
However, the command line options will override options supplied with the file.> The implementation of message passing interface (MPI) to python, mpi4py or pypar library can be used with pepgrep, which is included in pepgrep.mpi.py.
Besides descriptions of the implementation details, this section also describes the context in which the command line programs presented in this section can be used.
Column "command line" denotes that the software is accessible via command line interface, and "library" specifies that the implementation can be accessed via a specified software interface.
Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.
Availability and implementation: Poretools is an open-source software and is written in Python as both a suite of command line utilities and a Python application programming interface.
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