BenjaminSchwessinger / Honours

Repository for Honours work

2019/2020 Honours Project

Developing Tools for Fungal Pathogen Identification

Tavish Eenjes

This repository contains all data and code required for the project

Contents

• raw_data (Directory)
  • Contains the original raw fast5 data sourced from Yiheng
    • Contains subdirectories with the reads extracted from each .tar.gz file of raw reads
  • 20171103_FAH15473 (Directory)
    • P. striiformis tritici 79, Z. tritici WA332, P. tritici-repentis, F. oxysporum race3, T. brumale, C. globuliformis CM4, A. niger, C. lusitaniae, C. neoformans VN, P. chrysogenum, R. mucilaginosa, S. boydii
  • 20171207_FAH18654 (Directory)
    • B. proliferans, C. zeylanoides, G. geotrichum, K. ohmeri, M. guillermondii, W. anomalus, Y. mexicana, Y. scolyti, Y. lipolytica, Z. hellenicus, A. flavus
  • 20171212_FAH18688 (Directory)
    • C. zero CCL040, Aspergillus sp. CCL015, ??? ??? CCL067, Diaporthe sp., T. yallundae CCL031, T. yallundae CCL029, D vidmadera, Q. cyanescens CCL055, Entoleuca. sp. CCL052, ??? ??? CCL060, ??? ??? CCL068
  • 20180108_FAH18647 (Directory)
    • S. cerevisiae YH2Gold, Cladophialophora sp. CMM599, C. albicans, C. metapsilosis, C. orthopsilosis, C. parapsilosis, C. gatii VGIII, G. candidum, K. lactis, K. marxianus, P. kudriavzevii, P. membranifaciens
• analysis (Directory)
  • Contains all directories and files related to the data pre-processing and filtering
  • Deepbinned (Directory)
  • Contains all files generated by the Deepbinner software for demultiplexing the raw reads
    • 20171103_FAH15473 (Directory)
    • 20171207_FAH18654 (Directory)
    • 20171207_FAH18654 (Directory)
    • 20180108_FAH18647 (Directory)
      • barcode01, barcode02, barcode03, barcode04, barcode05, barcode06, barcode07, barcode08, barcode09, barcode10, barcode11, barcode12, unclassified (Directory) - Contains all fast5 reads for each barcode
  • Multi_fast5 (Directory)
  • Basecalled (Directory)
  • Filtering (Directory)
• scripts (Directory)
  • deepbinner_script.sh
    • Script for taking an input directory containing fast5 reads and processing them through Deepbinner, specifying an output directory
  • tensorflow_test.py
    • Script for testing whether TensorFlow, required for Deepbinner, is being run on CPU or GPU