Skip to content

version 0.0.1
Compare
Choose a tag to compare
@urmi-21 urmi-21 released this 29 Jan 23:14
· 326 commits to master since this release
0.0.1
56a2b08

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 (v. 2.9.6 or higher) SRA access
Trimgalore QC
BBDuk QC
Hisat2 Alignment
STAR Alignment
Bowtie2 Alignment
Kallisto Quant
Salmon Quant
Stringtie Transcript Assembly
Cufflinks Transcript Assembly
Trinity Transcript Assembly
Samtools Tools
Portcullis Tools
Mikado Tools
Assets 2
Loading