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    implementations of the cutadapt algorithm in Perl, Python, and C.

  testRNG_performance.pl
    This script tests different combinations of random number generators,
    and implementations of the inverse CDF method for sampling from
    truncated distributions. It's main output is a comma separated script of
    timing data.

  testsimsGSL.R
    This script is used to test the performance of the GSL RNGs against the
    inverse CDF implemented via a procedural logic in R. It outputs a single
    PNG file with the violin plots (a combination of box plots and kernel
    density) of the timing data for different possible implementations of
    the inverse CDF method in either R or Perl.

  vioplot_Perl_R_lognormal.png
    Performance comparison of Perl and R for the generation of truncated
    lognormal variates. It is produced by testsimsGSL.R

  testPerl.csv
    This is a CSV file that contains the timing data for the Perl RNGs and
    the inverse CDF method implemented in PDL. It is produced by
    testRNG_performance.pl

  perl_timing.txt
    This is a text file that contains the timing data for the various
    implementations of cutadapt in native Perl, PDL and PDL/C methods. It is
    produced by the script cutadapt_polyA_algo_timing.pl

  python_timing.txt
    This is a text file that contains the timing data for the various
    implementations of cutadapt in native Python. It is produced by the
    script cutadapt_polyA_algo_timing.py

SEE ALSO
    *   Bio::SeqAlignment <https://metacpan.org/pod/Bio::SeqAlignment>

        A collection of tools and libraries for aligning biological
        sequences from within Perl.

    *   cutadapt <https://metacpan.org/pod/Bio::SeqAlignment::cutadapt>

        This module provides an interface to the cutadapt tool for
        identifying and trimming adapters and primers from sequencing data.

    *   PDL <https://metacpan.org/pod/PDL>

        The Perl Data Language (PDL) gives standard Perl the ability to
        compactly store and speedily manipulate the large N-dimensional data
        arrays which are the bread and butter of scientific computing. PDL
        turns Perl into a free, array-oriented, numerical language that can
        be a very solid alternative to switching to Python or R for
        numerical computations during complex data analysis tasks and
        pipelines.

    *   polyester <https://github.com/alyssafrazee/polyester>

        Polyester is an R package designed to simulate RNA sequencing
        experiments with differential transcript expression.Given a set of
        annotated transcripts, Polyester will simulate the steps of an
        RNA-seq experiment (fragmentation, reverse-complementing, and
        sequencing) and produce files containing simulated RNA-seq reads.
        Simulated reads can be analyzed using your choice of downstream
        analysis tools. Polyester has a built-in wrapper function to
        simulate a case/control experiment with differential transcript
        expression and biological replicates. Users are able to set the
        levels of differential expression at transcripts of their choosing.
        This means they know which transcripts are differentially expressed
        in the simulated dataset, so accuracy of statistical methods for
        differential expression detection can be analyzed.

AUTHOR
    Christos Argyropoulos <chrisarg@cpan.org>

COPYRIGHT AND LICENSE
    This software is copyright (c) 2024 by Christos Argyropoulos.

    This is free software; you can redistribute it and/or modify it under
    the same terms as the Perl 5 programming language system itself.