assemblyPipeline.py

Introduction

assemblyPipeline.py is a wrapper for running de novo genome assembly analyses using the tools fastx_trimmer, cutadapt and fastq_quality_filter to prepare the data and the CLC Assembly Cell for the actual assembly.

Development notes

2013-02-08

The code is now working as intended. Input can be up to ten pairs of mate pair sequence files (in total 20 files). The number of files can easily be increased by changing the for loop that generates the value for variable self.files in class Conf.