BioC++

solving daily bioinformatic tasks
with C++ efficiently

René Rahn
Max Planck Institute for Molecular Genetics

Marcel Ehrhardt
Free University Berlin, de.NBI

Enrico Seiler
Max Planck Institute for Molecular Genetics

Schedule*:

14:00 - 14:30 Setup
14:30 - 15:00 Introduction Talk
15:00 - 15:30 FASTQ -> FASTA Conversion (sequence files)
15:30 - 15:45 Coffee Break
15:45 - 16:45 Simple Quality Filter (range / lambda / tuple)
16:45 - 17:00 Evaluation & Wrap-Up

Schedule*:

14:00 - 14:30 Setup
14:30 - 15:00 Introduction Talk
15:00 - 15:30 FASTQ -> FASTA Conversion (sequence files)
15:30 - 15:45 Coffee Break
15:45 - 16:45 Simple Quality Filter (range / lambda / tuple)
16:45 - 17:00 Evaluation & Wrap-Up

###### Setup build folder:

```bash
# configure & build:
cmake ../src/biocpp
# or alternatively
# cmake -DCMAKE_CXX_COMPILER=/path/to/g++ ../src/biocpp
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*:

14:00 - 14:30 Setup
14:30 - 15:00 Introduction Talk
15:00 - 15:30 FASTQ -> FASTA Conversion (sequence files)
15:30 - 15:45 Coffee Break
15:45 - 16:45 Simple Quality Filter (range / lambda / tuple)
16:45 - 17:00 Evaluation & Wrap-Up

Schedule*:

14:00 - 14:30 Setup
14:30 - 15:00 Introduction Talk
15:00 - 15:30 FASTQ -> FASTA Conversion (sequence files)
15:30 - 15:45 Coffee Break
15:45 - 16:45 Simple Quality Filter (range / lambda / tuple)
16:45 - 17:00 Evaluation & Wrap-Up

Schedule*:

14:00 - 14:30 Setup
14:30 - 15:00 Introduction Talk
15:00 - 15:30 FASTQ -> FASTA Conversion (sequence files)
15:30 - 15:45 Coffee Break
15:45 - 16:45 Simple Quality Filter (range / lambda / tuple)
16:45 - 17:00 Evaluation & Wrap-Up

Schedule*:

14:00 - 14:30 Setup
14:30 - 15:00 Introduction Talk
15:00 - 15:30 FASTQ -> FASTA Conversion (sequence files)
15:30 - 15:45 Coffee Break
15:45 - 16:45 Simple Quality Filter (range / lambda / tuple)
16:45 - 17:00 Evaluation & Wrap-Up

Next Event: SeqAn User Meeting

14^th September 2021, 16:00 - 19:00 CEST

BioC++

solving daily bioinformatic taskswith C++ efficiently

Schedule*:

Schedule*:

Schedule*:

Schedule*:

Schedule*:

Schedule*:

Schedule*:

Schedule*:

Next Event: SeqAn User Meeting

14th September 2021, 16:00 - 19:00 CEST

solving daily bioinformatic tasks
with C++ efficiently

14^th September 2021, 16:00 - 19:00 CEST