Scripts

OGApp.py

Python pipeline for Orthology Guided Assembly (OGA).

Dependencies: Python (2.6 or higher), Biopython, ncbi-blast+ (version > 2.2.26), pysam, math, sys, getopt, math, multiprocessing, subprocess

Please cite both:

  • Ruttink T, Sterck L, Rohde A, Bendixen C, RouzĂ© P, Asp T, Van de Peer Y, Roldan-Ruiz I (2013) Orthology Guided Assembly in highly heterozygous crops: creating a reference transcriptome to uncover genetic diversity in Lolium perenne. Plant Biotechnol J 11: 605-17
  • Bogaert KA, Beeckman T, De Clerck O (2017) Two-step cell polarization in algal zygotes. Nat Plants. doi: 10.1038/nplants.2016.221

https://github.com/kbogaert/OGApp.py

USAGE: python kbOGApp2.py -i <in contig file> -r <reference> -x <xmlfile> -n <threads> -e <evalue (10e-5)>