UM 2021

seqan/seqan3

Library Overview

• Quick Facts:
  • Sequence Analysis Library
  • C++17/20 Code with concepts
  • BSD 3-Clause License
  • v3.0.3
  • Mature Test Infrastructure
  • ~98% Code Coverage

• Alphabet Module
  • Biological Sequence Representation
  • Sequence Transformation

// 5′‑ATGCCACGAGTTGAC‑3′
seqan3::dna4_vector sequence{"ATGCCACGAGTTGAC"_dna4};

// 5′‑TACGGTGCTCAACTG‑3′
auto complement = sequence | seqan3::views::complement;

// 3′‑TACGGTGCTCAACTG‑5′ = "GTCAACTCGTGGCAT"_dna4
auto reverse_complement = complement | std::views::reverse;

// Met-Pro-Arg-Val-Asp = "MPRVD"_aa27
auto amino_acid_sequence = sequence
                         | seqan3::views::translate_single;

• Alignment Module
  • Pairwise Sequence Alignment
  • Different Algorithms depending on Configuration
  • Gapped Sequence Representation

• Alignment Configuration

auto scoring_scheme = seqan3::nucleotide_scoring_scheme{
    seqan3::match_score{4},
    seqan3::mismatch_score{-5}};

auto config =
    seqan3::align_cfg::method_global{} |
    seqan3::align_cfg::scoring_scheme{scoring_scheme} |
    seqan3::align_cfg::gap_cost_affine{
        seqan3::align_cfg::open_score{0},
        seqan3::align_cfg::extension_score{-1}
    } |
    seqan3::align_cfg::parallel{5} |
    seqan3::align_cfg::output_score |
    seqan3::align_cfg::output_alignment;

• Pairwise Sequence Alignment

auto sequence1 = "ATGCCACGAGTTGAC"_dna4;
auto sequence2 = "ACGCCACGAGTGAC"_dna4;
auto sequence_pair = std::tie(sequence1, sequence2);

auto alignments =
    seqan3::align_pairwise(sequence_pair, config);

for (seqan3::alignment_result & result: alignments)
{
    // ATGCCACGAGTTGAC
    // | ||||||||| |||
    // ACGCCACGAGT-GAC
    auto & [gapped_sequence1, gapped_sequence2]
        = result.alignment();

    // matches: 13, mismatches: 1, indel: 1
    // score: 13 * 4 + 1 * - 5 + 1 * -1 = 46
    std::signed_integral auto score = result.score();
}

• Search Module
  • Indexed Based Full-Text Search
  • Storing/Loading Indices
  • Different Algorithms depending on Configuration

• Index Creation

seqan3::dna4_vector genome{
    "ATCTGACGAAGGCTAGCTAGCTAAGGGA"_dna4};
seqan3::fm_index index{genome}; // build index

{ // storing the index
    std::ofstream os{"my_index.index", std::ios::binary};
    cereal::BinaryOutputArchive oarchive{os};
    oarchive(index);
}

{ // loading the index
    std::ifstream is{"my_index.index", std::ios::binary};
    cereal::BinaryInputArchive iarchive{is};
    iarchive(index);
}

• Search Configuration

auto config =
    seqan3::search_cfg::hit_all{} |
    seqan3::search_cfg::max_error_total{
        seqan3::search_cfg::error_count{1}} |
    seqan3::search_cfg::parallel{8} |
    seqan3::search_cfg::output_query_id{} |
    seqan3::search_cfg::output_reference_id{} |
    seqan3::search_cfg::output_reference_begin_position{};

• Full-Text Search

std::vector<seqan3::dna4_vector> queries{
    "GCT"_dna4, "ACCC"_dna4};

auto results = seqan3::search(queries, index, config);

for (seqan3::search_result & result : results)
{
    // 0 - GCT
    size_t query_id = result.query_id();

    // ATCTGACGAAGGCTAGCTAGCTAAGGGA
    // e.g. 11, 15, 19
    size_t position = result.reference_begin_position();
}

• Input/Output Module
  • Read/Write Files
  • Convert Files
  • File Formats
    • Sequence Files (.fa,.fq,.embl,.gbk)
    • SAM Files (.sam,.bam)

• Read Files

seqan3::sequence_file_input fin{"my.fastq"};

for (seqan3::sequence_record & record : fin)
{
    // e.g. "sequence1"
    std::string id = record.id();

    // e.g. "ATCTGACGAAGGCTAGCTAGCTAAGGGA"_dna5
    seqan3::dna5_vector sequence = record.sequence();

    // e.g. "##!!####!!####!!####!!####!!"_phred42
    std::vector<seqan3::phred42> qualities
        = record.base_qualities();
}

• Write Files

seqan3::sequence_file_input fin{"my.fastq"};
seqan3::sequence_file_output fout{"my.fasta"};

for (seqan3::sequence_record & record : fin)
{
    fout.push_back(record);
}

• Convert Files

seqan3::sequence_file_input fin{"my.fastq"};
seqan3::sequence_file_output fout{"my.fasta"};
fout = fin;

seqan/seqan3

Test Infrastructure

• Code Coverage

• Test Infrastructure

• API Stability
  • How to ensure that we do not break our API?
  • Idea:
    • Use the tests of the last release
    • and build them with the current library version.

seqan/seqan3

What's new?

• v3.0.3 statistics
• 7 months
• 11 contributors
• 923 commits
• 1,750 file changes
• 75,000 insertions / 50,000 deletions

• v3.0.3 milestones
• First release that should just compile^TM after upgrading
• We made a great push for the first stable v3.1.0 release!
• Declared many entities as API-stable / experimental

• v3.0.3 new features
• New Phred Quality Score alphabet seqan3::phred94
• New seqan3::literals namespace

  
              using namespace seqan3::literals;
              seqan3::dna4 adenine = 'A'_dna4;
          

• Records of I/O files have member functions

  
              seqan3::sequence_file_input fin{"my.fastq"};
  
              for (seqan3::sequence_record & record: fin)
                  std::cout << "id: " << record.id() << '\n';
          

seqan/seqan3

A peek at future releases

• v3.1.0
• Release Candidate v3.1.0-rc.1 already published.
• Basically v3.0.3, but without all the "deprecated" files.
• Will be the first "stable" Release.
• Last Release with g++-7/8 support.

• v3.2.x
• Requires ≥ g++-9.
• Will iron-out non-standard C++20 code.
• A re-write of our internal iterator/ranges/views implementation.
• Will support clang for the first time.
• And with that the complete llvm eco-system (hopefully).

seqan/app-template

• Standardized C++ Project Layout

  
  doc/        APP documentation
  include/    APP header files
  lib/        external libraries (default: SeqAn3)
  src/        APP source files
  test/       APP tests
  

• Open Software Stack:
  • CMake
  • GitHub Actions
  • BSD 3-Clause License

• Standardized test/

  
      api/        API tests
      benchmark/  Benchmarks
      cli/        CLI tests
      coverage/   Code Coverage
      data/       Test Data
      

• Reproducible Benchmarks

• Continuous integration (CI)
  • GitHub Actions
    • MacOS
    • Linux
    • Documentation

• Successful use cases:
  • SeqAn3 Apps
  • SeqAn2 Apps
  • C++ Library

• Future Features (planned):
  • App Template-Updater (PR on new Release)
  • Continuous Deployment (CD)
  • Easier deployment to

    
                git clone https://github.com/seqan/raptor
                mkdir raptor/build && cd raptor/build
                cmake ..
                make
                make install