Porechop | adapter trimmer for Oxford Nanopore reads

by rrwick C++ Version: v0.2.4 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | Porechop Summary

Porechop is a C++ library. Porechop has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

While I'm happy Porechop has so many users, it has always been a bit klugey and a pain to maintain. I don't have the time to give it the attention it deserves, so I'm going to now officially declare Porechop as abandonware (though the unanswered issues and pull requests reveal that it already has been for some time). I've added a known issues section to the README to outline what I think is wrong with Porechop and how a reimplementation should look. I may someday (no promises though :stuck_out_tongue:) try to rewrite it from a blank canvas to address its faults.

Support

Quality

Security

License

Reuse

Support

Porechop has a low active ecosystem.

It has 186 star(s) with 92 fork(s). There are 20 watchers for this library.

It had no major release in the last 12 months.

There are 42 open issues and 35 have been closed. On average issues are closed in 54 days. There are 6 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of Porechop is v0.2.4

Quality

Porechop has no bugs reported.

Security

Porechop has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

Porechop is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

Porechop releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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Porechop Key Features

No Key Features are available at this moment for Porechop.

Porechop Examples and Code Snippets

No Code Snippets are available at this moment for Porechop.

Community Discussions

Trending Discussions on Porechop

Snakemake: MissingInputException with inconsistent naming scheme

QUESTION

Snakemake: MissingInputException with inconsistent naming scheme

Asked 2020-Sep-10 at 15:23

I am trying to process MinION cDNA amplicons using Porechop with Minimap2 and I am getting this error.

...

ANSWER

Answered 2020-Sep-09 at 22:50

First of all, you can always debug the problems like that specifying the flag --printshellcmds. That would print all shell commands that Snakemake runs under the hood; you may try to run them manually and locate the problem.

As for why your rule doesn't produce any output, my guess is that samtools requires explicit filenames or - to use stdin:

Samtools is designed to work on a stream. It regards an input file '-' as the standard input (stdin) and an output file '-' as the standard output (stdout). Several commands can thus be combined with Unix pipes. Samtools always output warning and error messages to the standard error output (stderr).

So try that:

Source https://stackoverflow.com/questions/63818429

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install Porechop

Running the setup.py script will compile the C++ components of Porechop and install a porechop executable:.
If the last command complains about permissions, you may need to run it with sudo.
Install just for your user: python3 setup.py install --user If you get a strange "can't combine user with prefix" error, read this.
Install to a specific location: python3 setup.py install --prefix=$HOME/.local
Install with pip (local copy): pip3 install path/to/Porechop
Install with pip (from GitHub): pip3 install git+https://github.com/rrwick/Porechop.git
If you'd like to specify which compiler to use, set the CXX variable: export CXX=g++-6; python3 setup.py install
Porechop includes ez_setup.py for users who don't have setuptools installed, though that script is deprecated. So if you run into any installation problems, make sure setuptools is installed on your computer: pip3 install setuptools
By simply running make in Porechop's directory, you can compile the C++ components but not install an executable. The program can then be executed by directly calling the porechop-runner.py script.

Support

While I'm happy Porechop has so many users, it has always been a bit klugey and a pain to maintain. I don't have the time to give it the attention it deserves, so I'm going to now officially declare Porechop as abandonware (though the unanswered issues and pull requests reveal that it already has been for some time). I've added a known issues section to the README to outline what I think is wrong with Porechop and how a reimplementation should look. I may someday (no promises though :stuck_out_tongue:) try to rewrite it from a blank canvas to address its faults.

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