DrOmics Labs

Mastering Python : Beyond the Basics with Pipeline Engineering

About Course

Python Module I: Basics to Advanced

  • Introduction to Python language  
  • Role of Programming in Bioinformatics
  • Installation of Python on various platforms
  • Installation of IDE-Print function, Comments, User input
  • Command line arguments and Data types
  • Variables and rules to create a variable
  • In-built functions of Python slicing and indexing in String
  • String and data formatting
  • Control statements (if-else,If-elif-else,for loop, etc)
  • Python data structure (List, Set, Tuple, etc.)
  • Methods of data structures
  • Function introduction & its requirement
  • Exception Handling, File Handling & Pandas Library

Python Module II: Packages of Biopython

  • Introduction to Biopython
  • Installation of Biopython
  • Conversion of a string into a biological sequence
  • Obtaining complement, reverse complement, transcribe, reverse transcribe, and translation from a sequence
  • Finding GC content from a sequence
  • SeqIO object: Reading various biological file formats such as Fasta & GenBank
  • Analysis of fasta sequences
  • Finding GC content of a fasta file containing multiple sequences & storing the data in a file
  • Converting a GenBank file into Fasta format

Python Module III (APPLICATION:- NGS pipeline engineering using Biopython)

  • Introduction to RNA Seq  
  • Necessary Tools installation
  • Learn how Data Retrieval is done
  • Quality Check of reads
  • Trimming and cleaning of data
  • Understanding mapping of reads on the reference genome and file formats (SAM, BAM)
  • Visualization techniques
  • Gene Expression Quantification & Analyzation
  • Gene ontology enrichment analysis
  • RNA seq pipeline development
  • Pipeline automation of RNA sequencing pipeline using Python
Show More