Sequence analysis
11
NGS and TGS: principles
Fundamentals of computational biology
Preface
Introduction
The command line
1
The command line
2
Version control
3
Package managers
4
Notions of HPC
Intro. to algorithms
5
Algorithm thinking
6
Algorithm techniques
7
Data structures
Sequence analysis
8
Sequence analysis
9
Sanger analysis
10
Sequence alignments
11
NGS and TGS: principles
Phylogenetics
12
Phylogenetics
13
Phylogenomics
Genomics
14
Genome assembly
15
Genome annotation
16
Variant calling analysis
17
Comparative genomics
Metagenomics
18
Metagenomic sequencing
Structural bioinformatics
19
Structural bioinformatics
20
Molecular docking
Challenges
Unix challenges
Seq. Analysis challenges
Genome assembly
Appendix
History
References
Table of contents
11.1
Platforms yields
11.2
Reads main differences
11.3
Illumina principle (sequencing by synthesis)
11.3.1
The fastq format
11.3.2
Quality assesment of Illumina
11.4
PacBio principle (sequencing by incorporation)
11.4.1
Throughput evolution
11.4.2
Quality assesment of PacBio
11.5
Oxford Nanopore Technology (ONT) principle
11.5.1
Platforms
11.5.2
The fast5 file format
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11
NGS and TGS: principles
11.1
Platforms yields
11.2
Reads main differences
11.3
Illumina principle (sequencing by synthesis)
11.3.1
The fastq format
11.3.2
Quality assesment of Illumina
11.4
PacBio principle (sequencing by incorporation)
11.4.1
Throughput evolution
11.4.2
Quality assesment of PacBio
11.5
Oxford Nanopore Technology (ONT) principle
11.5.1
Platforms
11.5.2
The fast5 file format
10
Sequence alignments
12
Phylogenetics