temposeqcount, please add a reference of this paper if use in some form https://www.ncbi.nlm.nih.gov/pubmed/29163636

temposeqcount is analysis pipeline for TempO-Seq/RASL-Seq project that utilizes all next-generation sequencing platforms such as RADSeq. TempO-Seq allow targeted sequencing to high-throughput sample processing with the use of templates-dependent oligo ligation on 384 well plate. Knowing the number of reads mapped to the probes per well is the first step in the analysis. The application accept demultiplexed fastq folder and the manifest csv file that has probes and sample information to quantify the reads mapped to the probe per well in parallel.

The project attempt to streamline the analysis with all its dependencies handled.

It is an all-in-one solution, the tools uses many python packages and other dependencies. But,the application install the dependancies during installation. It include:

• Setuptools for distribution (Setuptools and Distribute have merged)
• Sphinx for documentation
• flake8 for source code checking
• pytest for unit testing
• mock for mocking (not required by the template, but included anyway)
• tox for testing on multiple Python versions

Follow the insturciton under the install link.

See Installation

See Changelog

Acknole

The Project supports the following versions out of the box:

• Python 2.6, 2.7
• Tested on Ubuntu 14.04, 15, 16.04 and CentOS-7

The code that makes temposeqcount is licensed under the GPL license. Feel free to use it in your free software/open-source.

Please report any bugs or requests that you have using the GitHub issue tracker!

I have tested on Python 2.7.

• Dereje Jima