https://github.com/msk-access/merge_fastq

Package to merge multiple pair of pair-end fastq data
https://github.com/msk-access/merge_fastq

fastq-files

Last synced: 4 months ago
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Package to merge multiple pair of pair-end fastq data

• Host: GitHub
• URL: https://github.com/msk-access/merge_fastq
• Owner: msk-access
• License: other
• Created: 2019-10-21T21:46:34.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-11-30T20:43:22.000Z (over 1 year ago)
• Last Synced: 2024-11-30T21:26:50.614Z (over 1 year ago)
• Topics: fastq-files
• Language: Python
• Homepage: https://merge-fastq.readthedocs.io
• Size: 66.4 KB
• Stars: 3
• Watchers: 2
• Forks: 1
• Open Issues: 14
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst

Awesome Lists containing this project

README

          
===========

merge_fastq

===========

.. image:: https://img.shields.io/pypi/v/merge_fastq.svg

        :target: https://pypi.python.org/pypi/merge_fastq

.. image:: https://travis-ci.com/msk-access/merge_fastq.svg?branch=master

    :target: https://travis-ci.com/msk-access/merge_fastq

.. image:: https://readthedocs.org/projects/merge-fastq/badge/?version=latest

        :target: https://merge-fastq.readthedocs.io/en/latest/?badge=latest

        :alt: Documentation Status

.. image:: https://pyup.io/repos/github/msk-access/merge_fastq/shield.svg

     :target: https://pyup.io/repos/github/msk-access/merge_fastq/

     :alt: Updates

Package to merge multiple pair of pair-end fastq data

* Free software: Apache Software License 2.0

* Documentation: https://merge-fastq.readthedocs.io.

Features

--------

* Given multiple pair-end fastq data merge them into single pair-end fastq w.r.t each READ1 and READ2 

Usage

-----

> merge_fastq --help

Usage: merge_fastq [OPTIONS]

  Console script for merge_fastq.

Options:

  -fp1, --fastq1 PATH      Full path to gziped READ1 fastq files, can be

                           specified multiple times for example: --fastq1

                           test_part1_R1.fastq.gz --fastq1

                           test_part2_R1.fastq.gz  [required]

  -fp2, --fastq2 PATH      Full path to gziped READ2 fastq files, can be

                           specified multiple times for example: --fastq2

                           test_part1_R2.fastq.gz --fastq2

                           test_part2_R2.fastq.gz  [required]

  -op, --output-path PATH  Full path to write the output files (default:

                           Current working directory)

  -of1, --out-fastq1 TEXT  Name of the merged output READ1 fastq file

                           (default: merged_fastq_R1.fastq.gz)

  -of2, --out-fastq2 TEXT  Name of the merged output READ2 fastq file

                           (default: merged_fastq_R2.fastq.gz)

  --help                   Show this message and exit.

Credits

-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter

.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage