Pandora's Toolbox for Bioinformatics
Pandora's Toolbox for Bioinformatics
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Pandora's Toolbox for Bioinformatics

Last updated on 2017-02-23

About the Book

About the Author

Homolog_us
Homolog_us

Homolog.us blog provides cutting-edge information on bioinformatics, transcriptomics and computational biology. Our tutorials provide simple introduction for biologists on algorithms related to assembly and analysis of next-generation sequencing. Here we are publishing the tutorials in book format for easy access.

Table of Contents

  • 1. Introduction
  • 2. List of programs
  • 3. Rationale for inclusion
  • 4. Server instructions
  • 5. Programs
  • 6. BLAST
    • 6.1 Quick instructions
    • 6.2 History
    • 6.3 Further readings
  • 7. BLAST tutorial
  • 8. How BLAST works
    • 8.1 BLAST score and E-value
    • 8.2 Score
    • 8.3 E-value
    • 8.4 Core Algorithms
    • 8.5 Rationale behind the Algorithm
    • 8.6 Increasing the Speed of Smith-Waterman
    • 8.7 Indexing
  • 9. BWA-MEM
    • 9.1 Quick instructions
    • 9.2 History
    • 9.3 Features
    • 9.4 Further readings
  • 10. BWA-MEM tutorial
  • 11. How BWAMEM works
    • 11.1 Details of algorithm
    • 11.2 Details of code
  • 12. FastTree
    • 12.1 Quick instructions
    • 12.2 History
    • 12.3 Further readings
  • 13. FastTree Tutorials
  • 14. How FastTree works
    • 14.1 Details of algorithm
    • 14.2 Details of code
    • 14.3 License
  • 15. HMMER
    • 15.1 Quick instructions
    • 15.2 History
    • 15.3 Further readings
  • 16. HMMER tutorials
  • 17. How HMMER works
    • 17.1 Algorithm
  • 18. Kallisto
    • 18.1 Quick instructions
    • 18.2 Features of Kallisto
    • 18.3 Further readings
  • 19. Kallisto Tutorial
  • 20. How Kallisto Works
    • 20.1 Algorithm
  • 21. KMC
    • 21.1 Quick instructions
    • 21.2 Features
    • 21.3 Further readings
  • 22. KMC tutorial
  • 23. How KMC works
    • 23.1 Details of algorithm
    • 23.2 Details of code
  • 24. Minimap and Miniasm
    • 24.1 Quick instructions
    • 24.2 History
    • 24.3 Further readings
  • 25. Minimap and miniasm tutorial
    • 25.1 Introduction
    • 25.2 Data files
    • 25.3 Commands
    • 25.4 Details
    • 25.5 Play
    • 25.6 Scaling
  • 26. How minimap and miniasm work
    • 26.1 Details of algorithm
  • 27. MUMMER
    • 27.1 Quick instructions
    • 27.2 Further readings
  • 28. MUMMER tutorial
  • 29. How MUMMER works
    • 29.1 Algorithm
  • 30. MUSCLE
    • 30.1 Quick instructions
    • 30.2 History
    • 30.3 Further readings
  • 31. MUSCLE tutorial
  • 32. How MUSCLE works
    • 32.1 Algorithm
  • 33. RAPSearch2
    • 33.1 Quick instructions
    • 33.2 History
    • 33.3 Further readings
  • 34. RAPSearch2 tutorials
  • 35. How RAPSearch2 works
    • 35.1 Details of algorithm
    • 35.2 Details of code
  • 36. Samtools
    • 36.1 History
  • 37. Samtools tutorials
  • 38. How samtools works
    • 38.1 Details of algorithm
    • 38.2 Details of code
  • 39. SPAdes
    • 39.1 Quick instructions
    • 39.2 History
    • 39.3 How to run
    • 39.4 Features of SPAdes
    • 39.5 Further readings
  • 40. SPAdes tutorial
  • 41. How SPAdes works
    • 41.1 Details of algorithm
  • 42. Trinity
    • 42.1 How to run
    • 42.2 History
    • 42.3 Further readings
  • 43. Trinity tutorial
  • 44. How Trinity works
    • 44.1 Details of algorithm
    • 44.2 Details of code

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