Mini Assembler

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Mini Assembler Software Project B SeqAn
David Weese and Prof. Knut Reinert
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SeqAn The C Sequence Analysis Library

• alphabets- scoring schemes- file formats-
  base pair probabilities-

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DNA Sequencing
Shotgun DNA Sequencing (Technology)
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Shotgun DNA Sequencing
Avg. Length 550 Avg. Error 1-2
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Project Mini Assembler
Input Reads (mate pairs), generated by a
simulator Goal Construct large scaffolds to
obtain a good assembly (N50 measure)
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Screener
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Screener
Mask known and de novo repeats
Task Build a repeat screener to help the
Overlapper
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Screener
Find overlaps between reads
Task Construct an overlapper module to compute
overlaps with affine gap costs.
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Screener
Compute consistent sub-assemblies (unitigs)
Task Construct overlap graph Construct a
spanning tree based layout
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Mated fragments
Screener
Build Scaffolds
Task Contruct mate pair contig graph Construct
scaffold with greedy approach
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Screener
Fill Gaps
Task Extend contigs using mates and overlaps
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Project Mini Assembler
Whole Genome Shotgun Assembly Pipeline
Screener
TTCGGGTTGAACGTGCATTAAATCGCGCAACTG
Compute consensus sequence and N50 score
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Names to Tasks
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Tasks

• Preferable requirements
• C/C skills
• C für Fortgeschrittene block seminar (6.4. -
  9.4.)
• Your work
• Collaborate and develop a module interface
• Make use of SeqAn - C Sequence Analysis
  Library (www.seqan.de)
• Implement your module in C
• Document your code
• Present your results
• Material
• Assembly lecture notes of Alg. Bioinformatik,
  Reinert WS07/08
• Links and documents on the homepage

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Schedule

• Seminar block 1 (2.4.)
• Introduction to principles of software design
• Tools (IDE, Debugger, Profiler, Bug Tracker,
  SVN, )
• Seminar block 2 (14.4. - 17.4.)
• SeqAn tutorial (Sequences, Alignments, Graphs,
  Indices)
• Assign names to tasks
• Make and present your plan (until 27.4.)
• Prepare a presentation
• What are your data types and interfaces to other
  modules?
• What algorithms you want to use?
• What do you use from SeqAn what do you implement
  new?
• Start Working
• Present your results, write a final report (until
  8.6.)

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End of Talk
Questions?
weese_at_inf.fu-berlin.de