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bioinformatics_programming_roadmap

The document outlines a 12-month roadmap for learning bioinformatics programming, starting with Python basics and advancing to complex topics such as data structures, algorithms, and bioinformatics tools. Each month focuses on specific skills, including data handling, visualization, and using R for statistical analysis. The final month emphasizes best practices in workflows, version control, and reproducible analysis.

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sidra bibi
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17 views

bioinformatics_programming_roadmap

The document outlines a 12-month roadmap for learning bioinformatics programming, starting with Python basics and advancing to complex topics such as data structures, algorithms, and bioinformatics tools. Each month focuses on specific skills, including data handling, visualization, and using R for statistical analysis. The final month emphasizes best practices in workflows, version control, and reproducible analysis.

Uploaded by

sidra bibi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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12-Month Bioinformatics Programming Roadmap

Month 1: Python Basics


• Variables, data types, and basic operations
• Lists, dictionaries, sets, and tuples
• Control flow: if statements, loops
• Functions and scoping
• File I/O: reading/writing text and CSV

Month 2: Python Intermediate


• Modules and packages; creating your own modules
• Virtual environments (venv/Conda)
• Exception handling (try/except)
• Basic testing with unittest or pytest

Month 3: Python Advanced


• Object-oriented programming (classes, inheritance)
• Decorators and context managers
• Concurrency: threading, multiprocessing, asyncio
• Performance profiling and optimization

Month 4: Python Data Handling & Visualization


• NumPy arrays and operations
• Pandas DataFrame: creation, indexing, grouping, merging
• Data cleaning and transformation
• Matplotlib & Seaborn: basic plotting

Month 5: Linux & Command Line


• File system navigation (ls, cd, cp, mv)
• Text processing with grep, awk, sed
• Shell scripting basics (Bash loops, variables)
• Software installation and package management

Month 6: Data Structures & Algorithms I


• Arrays & lists in Python and R
• String processing and regular expressions
• Searching and sorting algorithms
• Complexity analysis (Big-O notation)

Month 7: Data Structures & Algorithms II


• Trees and graphs fundamentals
• Dynamic programming (Needleman–Wunsch, Smith–Waterman)
• Suffix arrays/trees overview
• Algorithm optimization

Month 8: R Basics & Tidyverse


• R syntax: vectors, matrices, data frames
• Writing functions in R
• Data manipulation with dplyr and tidyr
• Working with factors and handling missing data

Month 9: R Visualization & Statistics


• ggplot2: grammar of graphics
• Descriptive statistics and distributions
• Hypothesis testing (t-tests, chi-squared)
• Regression analysis and multiple testing correction

Month 10: Biological File Formats & Parsing


• FASTA and FASTQ parsing with Biopython
• SAM/BAM handling with pysam or Rsamtools
• VCF reading and filtering
• GFF/GTF and BED file manipulation

Month 11: Bioinformatics Tools & Libraries


• Biopython and scikit-bio
• Bioconductor essentials (DESeq2, edgeR, GenomicRanges)
• Command-line tools: BLAST, HMMER, BWA, SAMtools
• Introduction to Docker/Singularity for environments

Month 12: Workflows & Best Practices


• Version control with Git and GitHub
• Modular coding and documentation
• Environment management (Conda, renv)
• Pipeline managers: Snakemake and Nextflow
• Reproducible analysis and testing

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