Home

Getting started

• Get to know SeqAn3 with our tutorial
• Build and testing our library

Important life hacks

• SSH -- ssh in connection with the fu-berlin servers

Guidelines

• Coding guideline Coding Guideline
• Documentation Guideline
• Git Guideline Git Guideline

General Reading

C++

On Modern C++ and design patterns used in SeqAn:

• SeqAn3 architecture -- Dissertation von Hannes Hauswedell
• Modern Cpp -- A list of recommended readings of modern C++
• CppSessions -- Slides to former cpp sessions about modern C++
• Concepts TS -- a small guide to C++ Concepts
• Dynamic and Static Polymorphism
• Ranges -- a small guide to C++ Ranges
• CRTP 🔗 -- the Curiously Recurring Template Pattern

Others

• Agile Project Execution -- Be an agile samurai ⚔️!
• Good Code Reviews🔗 -- worth reading
• SeqAn3 design decisions

Archive 2021-10: Old Wiki

Other links

• Weekly Todos -- Our Trello Board ❓

• Core Meeting notes -- Summary of strategy meetings for design decisions.

• Retrospectives -- How we conquer the world!

• Group Organization -- Never miss a meeting! ❓

• Ideas on Git Repository Structure ❓

• Continuous Integration -> sollte enrico neu schreiben

Modules

Documents on high-level design decisions in certain modules:

• Argument Parser seqan3/argument_parser
• Alphabet seqan3/alphabet
• ranges
  • Containers seqan3/containers
• Alignment seqan3/alignment
  • core
  • pairwise
  • pairwise (Myers)
  • multiple
  • score
• find
• graph
• search
• Indexes seqan3/index
• Input/Output seqan3/io
  • stream tokenisation, virtual_stream
  • Sequence (Fasta, Fastq...)
  • Alignment (SAM/BAM/CRAM, Blast)
  • Structure (vienna)
  • annotation (GTF, GFF...)

Drafts for new modules:

• Align module

External Submodules

• SDSL

Specifications

• I/O
  • Tokenization -- Specification of Tokenization
  • Stream -- Streams in SeqAn3