seqan/seqan3

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The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Stars: 463
Forks: 90
Open beginner issues: 0
Indexed issues: 31
Avg merge: 1h 11m
Merged PRs (30d): 3

Dominant language: C++
License: No license data
Last GitHub push: Sep 19, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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31 open issues indexed

type_name_as_string_test fails Open

bug

seqan/seqan3#3416 · 2 comments · 1 assignee · Opened Apr 14, 2026
Rare memory management failures in FM-index in multi-threadding context Open

bug

seqan/seqan3#3389 · 5 comments · 1 assignee · Opened Nov 7, 2025
Running sequence alignment with alphabets with more than 256 characters Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

seqan/seqan3#3341 · 3 comments · Opened Feb 19, 2025
Problem with installation on mac os x Open

question

seqan/seqan3#3286 · 5 comments · 1 assignee · Opened Sep 6, 2024
Improve SAM tag handling Open

feature/proposal

Difficulty 4/5 3-5 days Newbie friendliness 25/100

seqan/seqan3#3283 · Opened Aug 12, 2024
Score prealigned sequences Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

seqan/seqan3#3282 · Opened Aug 9, 2024
Multi-threading, banding, other speed-ups Open

question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

seqan/seqan3#3255 · 3 comments · Opened May 19, 2024
appending records to a .bam Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

seqan/seqan3#3250 · 1 comment · Opened Mar 5, 2024
single-thread mode Open

feature/proposal question

Difficulty 4/5 3-5 days Newbie friendliness 30/100

seqan/seqan3#3239 · 4 comments · Opened Feb 23, 2024
creating SAM file headers Open

documentation feature/proposal

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

seqan/seqan3#3235 · 1 comment · Opened Feb 16, 2024
Convert vertor<dna5> to std:string Open

question

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

seqan/seqan3#3218 · 1 comment · Opened Dec 17, 2023
output_sequence1_id and output_sequence2_id are same Open

bug

seqan/seqan3#3205 · 4 comments · 1 assignee · Opened Nov 8, 2023
alignment slice positions Open

question

Difficulty 3/5 1-2 days Newbie friendliness 25/100

seqan/seqan3#3203 · 1 comment · Opened Nov 1, 2023
several same-score pairwise alignments Open

question

Difficulty 5/5 Over a week Newbie friendliness 35/100

seqan/seqan3#3198 · 6 comments · Opened Oct 11, 2023
Tests fail to compile Open

bug response needed

Difficulty 3/5 1-2 days Newbie friendliness 25/100

seqan/seqan3#3191 · 2 comments · Opened Sep 10, 2023
Use OS/system packaged sdsl library Open

question

Difficulty 3/5 1-2 days Newbie friendliness 35/100

seqan/seqan3#3162 · 10 comments · Opened Jul 2, 2023
[Alignment] Is there a way to run align_pairwise without traceback? Open

question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

seqan/seqan3#3045 · 3 comments · Opened Aug 12, 2022
[IO] BAM index support Open

feature/proposal

Difficulty 5/5 Over a week Newbie friendliness 25/100

seqan/seqan3#2985 · 6 comments · Opened May 21, 2022
[IO] VCF/BCF support Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

seqan/seqan3#2953 · 2 comments · Opened Mar 26, 2022
[Alphabet] seqan3::concatenated_sequences benchmark Open

ready to tackle

seqan/seqan3#2951 · 7 comments · 1 assignee · Opened Mar 21, 2022
[Search] Query the text size Open

feature/proposal

Difficulty 4/5 3-5 days Newbie friendliness 35/100

seqan/seqan3#2934 · 1 comment · Opened Jan 26, 2022
[IO] Access list of file extensions of seqan3 I/O input classes Open

feature/proposal

Difficulty 3/5 1-2 days Newbie friendliness 45/100

seqan/seqan3#2927 · 1 comment · Opened Jan 10, 2022
[Search] XOR Filters Open

feature/proposal

Difficulty 5/5 Over a week Newbie friendliness 20/100

seqan/seqan3#2925 · 11 comments · Opened Jan 7, 2022
[IO] Parsing for genome alignment formats (MAF and HAL) Open

feature/proposal

Difficulty 5/5 Over a week Newbie friendliness 25/100

seqan/seqan3#2903 · 6 comments · Opened Nov 25, 2021
[Search] Shapes are the wrong way around Open

question

seqan/seqan3#2832 · 8 comments · 1 assignee · Opened Sep 24, 2021
[Alphabet] Alphabet types can no longer be constructed using their rank Open

documentation ready to tackle

Difficulty 4/5 3-5 days Newbie friendliness 25/100

seqan/seqan3#2745 · 12 comments · 1 reaction · Opened Jun 9, 2021
[IO] Is there a neat way to pass only selected fields to SAM output? Open

documentation question ready to tackle

seqan/seqan3#2436 · 4 comments · 1 assignee · Opened Mar 9, 2021
[Infra] Python bindings Open

feature/proposal

Difficulty 5/5 Over a week Newbie friendliness 15/100

seqan/seqan3#2232 · 1 comment · 2 reactions · Opened Nov 2, 2020
[Alignment] Multiple Sequence Alignment (MSA) and Alignment Graph Open

feature/proposal

Difficulty 5/5 Over a week Newbie friendliness 25/100

seqan/seqan3#1763 · 10 comments · Opened Apr 24, 2020
[Infra] Use SIMD Everywhere Open

feature/proposal

Difficulty 4/5 3-5 days Newbie friendliness 35/100

seqan/seqan3#1391 · 3 comments · Opened Nov 29, 2019
[Alignment] Meta-issue Open

seqan/seqan3#314 · 7 comments · 2 assignees · Opened Aug 1, 2018

seqan/seqan3

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