nanofilt | Filtering and trimming of long read sequencing data | Genomics library

by wdecoster Python Version: 2.8.0 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | nanofilt Summary

nanofilt is a Python library typically used in Artificial Intelligence, Genomics applications. nanofilt has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install nanofilt' or download it from GitHub, PyPI.

Filtering and trimming of long read sequencing data. Filtering on quality and/or read length, and optional trimming after passing filters. Reads from stdin, writes to stdout. Optionally reads directly from an uncompressed file specified on the command line.

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Security

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Support

nanofilt has a low active ecosystem.

It has 150 star(s) with 13 fork(s). There are 9 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 54 have been closed. On average issues are closed in 137 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of nanofilt is 2.8.0

Quality

nanofilt has 0 bugs and 0 code smells.

Security

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

nanofilt code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

nanofilt 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

nanofilt releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

kandi has reviewed nanofilt and discovered the below as its top functions. This is intended to give you an instant insight into nanofilt implemented functionality, and help decide if they suit your requirements.

Filter fastq files based on summary
Calculate the average quality of a sequence
Argument parser
Filter fastq files based on command line options
Return True iff the time range is less than tto

Get all kandi verified functions for this library.

nanofilt Key Features

No Key Features are available at this moment for nanofilt.

nanofilt Examples and Code Snippets

No Code Snippets are available at this moment for nanofilt.

Community Discussions

Trending Discussions on nanofilt

Mix shell command in environment conda with python scripts in snakemake tool

Snakemake tries to run rule, reason: Missing output files, but files are temporary

QUESTION

Mix shell command in environment conda with python scripts in snakemake tool

Asked 2020-Sep-27 at 00:17

I would like to mix shell command in environment conda with any Python scripts, so the use of the 'run' section isn't possible ...

I tried :

...

ANSWER

Answered 2020-Sep-17 at 15:44

Snakemake shell doesn't support bash syntax for loops. I see two possible solutions.

First, you may wrap this code into a .sh file and run that from the shell section:

Source https://stackoverflow.com/questions/63917484

QUESTION

Snakemake tries to run rule, reason: Missing output files, but files are temporary

Asked 2020-Jul-17 at 08:40

I have a series of rule leading into using vsearch, with the barebones shown here:

...

ANSWER

Answered 2020-Jul-17 at 08:40

I would move seqkit fq2fa to its own rule producing the temp file nedded by vsearch. Like (not tested):

Source https://stackoverflow.com/questions/62942329

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

Vulnerabilities

No vulnerabilities reported

Install nanofilt

NanoFilt is written for Python 3.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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