General info

|n this part of the Practical course sequence analysis you will be confronted with the situation of prototyping NGS analysis programs with an available C++ library of effiecient data types and algorithms, namly SeqAn.

Date	Content	Lecturer
05.06	Introduction to SeqAn	Knut Reinert, Jochen Singer
12.06	Programming NGS tools in SeqAn	Jochen Singer

Day 1 (05.06)

• General introduction of goals of this unit
• Assignment 1: Install SeqAn on your computer (follow instructions here)
• Assignment 2: Work through First steps tutorial with guidance.
• Assignment 3: Program first app with the command line parser
• Assignment 4: Work through the sequence IO Tutorial
• Assignment 5: Adapt your first app, such that it can read fastq files.
• Assignment 6: Program a simple quality trimming (easy version: just cut a number of bases at the end)
  • (optional): Make you functions template functions (such that they can be reused)
  • (optional): Adapt the trimming function from the trimmer such that all bases from the end are removed which are below a certain threshold.
  • (optional): optional: Adapt the trimming function from the trimmer such that a window of a specified length is shifted from the begin to the end of the read and the average quality of the window is used to trim the read.

Day 2 (12.06)

• Introduction to adapter removal, read mapping
• Assignment 1: Program de-multiplexer removal
  • Write a simple de-multiplexer that retrieves all reads with a certain barcode
  • The barcode has to be provided by a file
  • (optional) Use a file with multiple barcodes (only select a read if it is the best match to the specified adaptor)
  • (optional) Use a file with multiple barcodes and create several output files, one for each adaptor
• Assignment 2: Program a adapter removal tool
  • Sometimes part of the adapter is contaminating a read and therefore has to be removed
  • Write an app (such as the quality trimmer) that reads a read file, removes adaptors from the reads and writes the result to a file.
  • The adapter sequence can either be read from file or taken from the command line.
  • (optional) Allow errors in the adapter sequence.
• Assignment 3: Work through the index tutorial
• Assignment 4: Program simple read mapper
  • The app should be based on a seed and extend approach
  • Create the seeds (pigeon-principle)
  • Search for seed with the help of an index
  • Verify the seeds - write a simple function which compares two sequences (or use the globalAlignment() function)
  • (optinal) Implement the verification with Myers verification
  • (optinal) Adjust the range of the verification to take edit distance into consideration
  • (optinal) Try different indices (the app should be based on templates)
  • (optinal) Implement a strategy to optimize the number of verifications.

Resources and links

• SeqAn home
• SeqAn reference manual
• Trac with tutorials
• C++ reference and info

• fastq with DNA and DNA5

Solutions

• Quality trimming
• AdapterRemoval

Sources

• Reads