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Wing-Kin Sung Solution handbook for Algorithms for Next-Generation Sequencing 1 / 4
Contents
- Introduction 1
- NGS le formats 3
- Related algorithms and data structures 5
- NGS read mapping 15
- Genome Assembly 29
- Single nucleotide variation (SNV) calling 39
- Structural Variation calling 47
- RNA-seq 53
- Peak calling methods 57
10 Data compression techniques used in NGS les 61 iii 2 / 4
Chapter 1 Introduction
- Consider the DNA sequence 5'-ACTCAGTTCG-3'. What is its reverse
complement? The SOLiD sequencer will output color-based sequences.What is the expected color-based sequence for the above DNA sequence and its reverse complement? Do you observe an interesting property?
Solution:The reverse complement is 5'-CGAACTGAGT-3'.
The color-based sequences for the DNA sequence and its reverse com- plement are A122121023 and C320121221. If the original DNA sequence isS, its reverse complement is reverse ofS.
- Should we always use second- or third- generation sequencing instead of
rst-generation sequencing? If not, when should we use Sanger sequenc- ing?
Solution:If we only want verify the sequence of a few DNA fragments,
it is cheaper to use Sanger sequencing.
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- Solution handbook for Algorithms for Next-Generation Sequencing
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