Thesis on CuriousCoding

Thesis: Optimal Throughput Bioinformatics

Thu, 10 Apr 2025 00:00:00 +0200

Table of Contents

Abstract
1 Introduction
2 Discussion
- 2.1 Pairwise Alignment
- 2.2 Low Density Minimizers
- 2.3 High Throughput Bioinformatics
- 2.4 Propositions

This post contains the abstract, introduction, and conclusion of my thesis (Groot Koerkamp 2025a). The full PDF is here. Individual chapters are based on blog posts and/or papers and introduced in detail in the introduction below. In brief:

A History of Pairwise Alignment

Wed, 09 Apr 2025 00:00:00 +0200

Table of Contents

1 A Brief History
- 1.1 A*PA
- 1.2 A*PA2
- 1.3 Overview
2 Problem Statement
3 Alignment types
4 Cost Models
- 4.1 Minimizing Cost versus Maximizing Score
5 The Classic DP Algorithms
6 Linear Memory using Divide and Conquer
7 Dijkstra’s Algorithm and A*
8 Computational Volumes and Band Doubling
9 Diagonal Transition
10 Parallelism
11 LCS and Contours
12 Some Tools
13 Subquadratic Methods and Lower Bounds
14 Summary

This is Chapter 2 of my thesis (Groot Koerkamp 2025), to introduce the first part on Pairwise Alignment. Please cite the thesis instead of this post.

Low Density Minimizers

Tue, 08 Apr 2025 00:00:00 +0200

Table of Contents

1 Theory of Sampling Schemes
- 1.1 Introduction
- 1.2 Overview
- 1.3 Theory of sampling schemes
- 1.4 Notation
- 1.5 Types of sampling schemes
- 1.6 Computing the density
- 1.7 The density of random minimizers
- 1.8 Universal hitting sets
- 1.9 Asymptotic results
- 1.10 Variants
2 Lower Bounds on Sampling Scheme Density
3 Practical Sampling Schemes
- 3.1 Variants of lexicographic minimizers
  - Evaluation
- 3.2 UHS-inspired schemes
- 3.3 Syncmer-based schemes
- 3.4 Open-closed minimizer
  - Evaluation
- 3.5 Mod-minimizer
  - Theoretical density
  - Evaluation
- 3.6 Discussion
4 Towards Optimal Selection Schemes
- 4.1 Bidirectional anchors
- 4.2 Sus-anchors
  - Evaluation
- 4.3 Discussion

This is Part 2 of my thesis (Groot Koerkamp 2025), containing chapters 6 to 9 on Low Density Minimizers. Please cite the thesis instead of this post.

Beyond Global Alignment

Mon, 07 Apr 2025 00:00:00 +0200

Table of Contents

1 Variants of semi-global alignment
2 Fast text searching
- 2.1 Skip-cost for overlap alignments
- 2.2 Results
3 Mapping using A*Map
- 3.1 Seeding
- 3.2 Chaining
- 3.3 Aligning
- 3.4 A*Map
- 3.5 Results

This is Chapter 5 of my thesis (Groot Koerkamp 2025). Please cite the thesis instead of this post.

Summary

So far, we have considered only algorithms for global alignment. In this chapter, we consider semi-global alignment and its variants instead, where a pattern (query) is searched in a longer string (reference). There are many flavours of semi-global alignment, depending on the (relative) sizes of the inputs. We list these variants, and introduce some common approaches to solve this problem.

High Throughput Bioinformatics

Sun, 06 Apr 2025 00:00:00 +0200

Table of Contents

1 Introduction
- 1.1 Overview
2 Optimizing Compute Bound Code: Random Minimizers
- 2.1 Avoiding Branch Misses
- 2.2 SIMD: Processing In Parallel
- 2.3 Instruction Level Parallelism
- 2.4 Input Format
3 Optimizing Memory Bound Code: Minimal Perfect Hashing
- 3.1 Using Less Memory
- 3.2 Reducing Memory Accesses
- 3.3 Interleaving Memory Accesses
- 3.4 Batching, Streaming, and Prefetching

This is Chapter 10 of my thesis (Groot Koerkamp 2025a), to introduce the last part on High Throughput Bioinformatics.