Owner

seqan

11 indexed repositories · View on GitHub

seqan
SeqAn's official repository.

C++ · 502 stars
seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

C++ · 463 stars
raptor
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

C++ · 55 stars
needle
A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences

C++ · 16 stars
sharg-parser
The modern argument parser for c++ tools

C++ · 11 stars
chopper
A tool for partitioning a set of sequences into similar batches.

C++ · 10 stars
app-template
This template comes pre-configured with various SeqAn libraries and a basic Continuous Integration setup. It is designed to provide a rob...

CMake · 6 stars
hibf
HIBF and IBF

C++ · 5 stars
dream-stellar
Fast and exact local alignments

C++ · 4 stars
hibf_benchmarks
WIP HIBF benchmarks

Python · 0 stars
www.seqan.de

SCSS · 0 stars

Beginner friendly Everything

Open All

Semi-global alignment with local-style termination (max over all cells) — achievable ? Open

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

seqan/seqan#2590 · 3 comments · Opened May 29, 2026
type_name_as_string_test fails Open

bug

seqan/seqan3#3416 · 2 comments · 1 assignee · Opened Apr 14, 2026
Build stops if no k-mers in minimiser file Open

enhancement

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

seqan/raptor#546 · Opened Feb 24, 2026
Support --kmer-count-cutoff on build/update Open

enhancement

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

seqan/raptor#545 · Opened Feb 24, 2026
Support minimiser file on update insert Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

seqan/raptor#544 · 2 comments · Opened Feb 24, 2026
Follow-up: Auto-Synopsis on macOS Open

bug

seqan/sharg-parser#303 · 1 assignee · Opened Jan 24, 2026
AVX512 follow-ups Open

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

seqan/hibf#307 · Opened Nov 25, 2025
Rare memory management failures in FM-index in multi-threadding context Open

bug

seqan/seqan3#3389 · 5 comments · 1 assignee · Opened Nov 7, 2025
Add CMake Presets Open

seqan/app-template#139 · 1 assignee · Opened Sep 4, 2025
Razers3 gives empty results.razers file even when testing with simple items? Open

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

seqan/seqan#2562 · 1 comment · Opened Jul 3, 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
Exception in banded refine alignment Open

bug

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

seqan/seqan#2540 · 4 comments · Opened Dec 7, 2024
Mason simulator - generate error free illumina reads Open

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

seqan/seqan#2534 · 1 comment · Opened Oct 31, 2024
Mason Simulator Segmentation fault Open

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

seqan/seqan#2533 · Opened Oct 24, 2024
Distributed search Open

enhancement

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

seqan/dream-stellar#118 · Opened Oct 3, 2024
data_store follow-ups Open

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

seqan/hibf#227 · Opened Sep 10, 2024
Problem with installation on mac os x Open

question

seqan/seqan3#3286 · 5 comments · 1 assignee · Opened Sep 6, 2024
Landing Page Open

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

seqan/hibf_benchmarks#37 · Opened Aug 13, 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
Issue with Generating Layout File in Chopper and Inputting into Raptor Build Index Open

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

seqan/raptor#420 · 1 comment · Opened Jun 28, 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
[MISC] Layout object structure of user bins. Open

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

seqan/hibf#191 · Opened Jan 18, 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
Revise directory structure Open

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

seqan/hibf#177 · Opened Dec 1, 2023
Do not write empty Stellar files Open

enhancement

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

seqan/dream-stellar#102 · Opened Nov 22, 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
Reallow setting hash and fpr Open

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

seqan/raptor#382 · Opened Sep 15, 2023
Investigative Todos Open

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

seqan/hibf#89 · 1 reaction · Opened Sep 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
HIBF creates a very large index Open

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

seqan/raptor#370 · 3 comments · Opened Sep 1, 2023
String identifier for user bins Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

seqan/raptor#356 · 1 comment · Opened Aug 3, 2023
[MISC] Display layout Open

seqan/chopper#191 · 2 comments · 1 assignee · Opened Jul 28, 2023
Todos Open

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

seqan/hibf#38 · 1 comment · Opened Jul 6, 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
To-do: Changes that affect serialization Open

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

seqan/raptor#314 · Opened May 9, 2023
Add examples for --input / --output parameters Open

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

seqan/raptor#270 · Opened Feb 28, 2023
Update documentation Open

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

seqan/raptor#245 · Opened Feb 3, 2023
Backlog Open

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

seqan/raptor#236 · Opened Feb 1, 2023
[suggestion] Check that `.parse()` is called. Open

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

seqan/sharg-parser#168 · 7 comments · Opened Jan 3, 2023
Add parameter `--skip-similarity-preprocessing`. Open

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

seqan/chopper#122 · 1 comment · Opened Dec 13, 2022
Add a mechanism to allow integer to specify orders of magnitude suffixes like k, m, g, t? Open

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

seqan/sharg-parser#165 · 1 comment · Opened Nov 17, 2022
Too strict validators Open

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

seqan/sharg-parser#161 · 3 comments · Opened Nov 9, 2022
"needle" name conflict Open

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

seqan/needle#128 · Opened Nov 2, 2022
help text: std types should be renamed Open

seqan/sharg-parser#153 · 3 comments · 1 assignee · Opened Oct 20, 2022

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