view release on metacpan or  search on metacpan

README  view on Meta::CPAN

        start with a primer sequence. Poly-A tails are useful for pulling
        out RNA from your sample, but often you don't want them to be in
        your reads.

        Cutadapt helps with these trimming tasks by finding the adapter or
        primer sequences in an error-tolerant way. It can also modify and
        filter single-end and paired-end reads in various ways. Adapter
        sequences can contain IUPAC wildcard characters. Cutadapt can also
        demultiplex your reads.

    *   pipx <https://pipx.pypa.io/stable/>

        pipx is a tool to help you install and run end-user applications
        written in Python. It's roughly similar to macOS's brew,
        JavaScript's npx, and Linux's apt.

        It's closely related to pip. In fact, it uses pip, but is focused on
        installing and managing Python packages that can be run from the
        command line directly as applications.

        How is it Different from pip?

        pip is a general-purpose package installer for both libraries and
        apps with no environment isolation. pipx is made specifically for
        application installation, as it adds isolation yet still makes the
        apps available in your shell: pipx creates an isolated environment
        for each application and its associated packages.

        pipx does not ship with pip, but installing it is often an important
        part of bootstrapping your system.

    *   Homebrew <https://brew.sh/>

        Homebrew installs the stuff you need that Apple (or your Linux
        system) didn't.

    *   Scoop <https://scoop.sh/>

        Scoop is a command-line installer for Windows that: *Eliminates
        permission popup windows *Hides GUI wizard-style installers
        *Prevents PATH pollution from installing lots of programs *Avoids
        unexpected side-effects from installing and uninstalling programs
        *Finds and installs dependencies automatically *Performs all the
        extra setup steps itself to get a working program

    *   Alien

lib/Alien/SeqAlignment/cutadapt.pm  view on Meta::CPAN

sequence. Poly-A tails are useful for pulling out RNA from your sample,
but often you don't want them to be in your reads.

Cutadapt helps with these trimming tasks by finding the adapter or
primer sequences in an error-tolerant way. It can also modify and filter
single-end and paired-end reads in various ways. Adapter sequences can
contain IUPAC wildcard characters. Cutadapt can also demultiplex your
reads.


=item * L<pipx|https://pipx.pypa.io/stable/>

pipx is a tool to help you install and run end-user applications written 
in Python. It's roughly similar to macOS's brew, JavaScript's npx, and
Linux's apt.

It's closely related to pip. In fact, it uses pip, but is focused on 
installing and managing Python packages that can be run from the command
line directly as applications. 

How is it Different from pip?

pip is a general-purpose package installer for both libraries and apps 
with no environment isolation. pipx is made specifically for application
installation, as it adds isolation yet still makes the apps available in
your shell: pipx creates an isolated environment for each application
and its associated packages.

pipx does not ship with pip, but installing it is often an important
part of bootstrapping your system.

=item * L<Homebrew|https://brew.sh/>

Homebrew installs the stuff you need that Apple (or your Linux system) didn't.

=item * L<Scoop|https://scoop.sh/>

Scoop is a command-line installer for Windows that:
*Eliminates permission popup windows
*Hides GUI wizard-style installers
*Prevents PATH pollution from installing lots of programs
*Avoids unexpected side-effects from installing and uninstalling programs
*Finds and installs dependencies automatically
*Performs all the extra setup steps itself to get a working program

=item * L<Alien>