First release
pyrpipe: python rna-seq pipeliner
Introduction
pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop RNA-Seq analyses workflow by integrating popular RNA-Seq analysis programs in an object oriented manner.
pyrpipe can be used on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-use APIs to popular bioinformatic tools provided
with pyrpipe, or can use the methods provided in the pyrpipe_engine module to integrate any other third-party program in their pipeline.
What it does
Allows fast and easy development of bioinformatics pipelines in python by providing
* a high level api to popular bioinformatics tools
* a general api to execute any linux command from python (using the subprocess module)
* comprehensive logging features to log all the commands, output and their return status
* report generating features for easy sharing, reproducing, benchmarking and debugging
Prerequisites
* python 3.6 or higher
* OS: Linux, Mac
pyrpipe provides API to:
| Tool | Purpose |
|--------------------------------------------------------------------------------------|---------------------|
| [SRA Tools](https://github.com/ncbi/sra-tools) (v. 2.9.6 or higher) | SRA access |
| [Trimgalore](https://github.com/FelixKrueger/TrimGalore) | QC |
| [BBDuk](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) | QC |
| [Hisat2](https://ccb.jhu.edu/software/hisat2/index.shtml) | Alignment |
| [STAR](https://github.com/alexdobin/STAR) | Alignment |
| [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) | Alignment |
| [Kallisto](https://pachterlab.github.io/kallisto/) | Quant |
| [Salmon](https://combine-lab.github.io/salmon/) | Quant |
| [Stringtie](https://github.com/gpertea/stringtie) | Transcript Assembly |
| [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) | Transcript Assembly |
| [Trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki) | Transcript Assembly |
| [Samtools](https://github.com/samtools/samtools) | Tools |
| [Portcullis](https://github.com/maplesond/portcullis) | Tools |
| [Mikado](https://github.com/EI-CoreBioinformatics/mikado) | Tools |