SeqAn - From an Idea to a Single Tool

From an Idea to a single tool
(Read Mapper)

Marcel Ehrhardt
Free University Berlin, de.NBI

Enrico Seiler
Max Planck Institute for Molecular Genetics

Schedule*:

16:00 - 16:45 Introduction to SeqAn
16:45 - 17:15 SetUp
17:15 - 17:30 Short Break
17:30 - 18:45 Read Mapper
18:45 - 19:00 Evaluation & Wrap-Up

Schedule*:

16:00 - 16:45 Introduction to SeqAn
16:45 - 17:15 SetUp
17:15 - 17:30 Short Break
17:30 - 18:45 Read Mapper
18:45 - 19:00 Evaluation & Wrap-Up

###### Setup build folder:

```bash
# configure & build:
cmake ../src/read_mapper
# or alternatively
# cmake -DCMAKE_CXX_COMPILER=/path/to/g++ ../src/read_mapper
make -j 4
```

<pre class="fragment"><code class="language-bash hljs" style="max-height: 300px">-- The CXX compiler identification is GNU 11.1.0
-- Check for working CXX compiler: /usr/bin/g++-11
-- Check for working CXX compiler: /usr/bin/g++-11 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Finding SeqAn3 and checking requirements:
--   SeqAn3 include dir found:   /home/biocpp/learning-resources/submodules/seqan3/include
--   Detected as running from a repository checkout…
--     …adding submodule include:  /home/biocpp/learning-resources/submodules/seqan3/submodules/cereal/include
--     …adding submodule include:  /home/biocpp/learning-resources/submodules/seqan3/submodules/range-v3/include
--     …adding submodule include:  /home/biocpp/learning-resources/submodules/seqan3/submodules/sdsl-lite/include
--   C++ Standard-17 support:    builtin
--   C++ Concepts support:       via -std=c++20
--   C++ Filesystem header:      &lt;filesystem>
--   C++ Filesystem library:     builtin
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
--   Thread support:             via -pthread
--   Required dependency:        Range-V3 found.
--   Required dependency:        SDSL found.
--   Optional dependency:        Cereal found.
--   Optional dependency:        Lemon not found.
--   Optional dependency:        ZLIB-1.2.11 found.
--   Optional dependency:        BZip2-1.0.8 found.
--   Optional dependency:        libexecinfo found.
--   SeqAn3 platform.hpp build:  passed.
-- Found SeqAn3: /home/biocpp/learning-resources/submodules/seqan3/include (Required is at least version "3.0.3")
-- Configuring done
-- Generating done
-- Build files have been written to: /home/biocpp/learning-resources/build
</code></pre>

Schedule*:

16:00 - 16:45 Introduction to SeqAn
16:45 - 17:15 SetUp
17:15 - 17:30 Short Break
17:30 - 18:45 Read Mapper
18:45 - 19:00 Evaluation & Wrap-Up

How does a read mapper work?

Read Mapper

Reference Sequence

Read Mapper

Query Sequence

Read Mapper

Find rough position in reference sequence

Read Mapper

Rough position of query within reference

Read Mapper

Align query with reference window

Read Mapper

Read Mapper: What do we need?

We need an indexer (to create an FM-index)
We need a mapper (uses the FM-index)

Indexer

Mapper

Schedule*:

16:00 - 16:45 Introduction to SeqAn
16:45 - 17:15 SetUp
17:15 - 17:30 Short Break
17:30 - 18:45 Read Mapper
18:45 - 19:00 Evaluation & Wrap-Up

@SeqAnLib

github/seqan

seqan.de

From an Idea to a single tool(Read Mapper)

Schedule*:

Schedule*:

Schedule*:

How does a read mapper work?

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper

Read Mapper: What do we need?

Indexer

Indexer

Indexer

Indexer

Indexer

Indexer

Indexer

Indexer

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Mapper

Schedule*:

From an Idea to a single tool
(Read Mapper)