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Citing

SeqAn is a research project and depends strongly on being correctly attributed. Please always cite the correct research papers when you develop software based on SeqAn. This will help us continue to acquire funding and improve the library.

# Publications

SeqAn3 has not yet been published academically, for now cite SeqAn2:

Publication |
--- | ---
Title | The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.
Year | 2017
Authors | Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., ... & Urgese, G.
Journal | Journal of biotechnology, 261, 157-168
Links | original

Certain compontents of SeqAn are published separately. If you make strong use of one of those compononts and/or specifically compare to that component, please cite the respective publication additionally.

## Alignment module

Publication |
--- | ---
Title | Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.
Year | 2018
Authors | Rahn, R., Budach, S., Costanza, P., Ehrhardt, M., Hancox, J., & Reinert, K
Journal | Bioinformatics, 34(20), 3437-3445
Links | original

Cite the above publication when you make strong use of the alignment module, in particular if you rely on the high-performance computing capabilities.

## Search module

Publication |
--- | ---
Title | From theory to practice: Plug and play with succinct data structures.
Year | 2014
Authors | Gog, S., Beller, T., Moffat, A., & Petri, M.
Journal | International Symposium on Experimental Algorithms (pp. 326-337). Springer, Cham.
Links | original

Full text indexing in SeqAn3 makes use of the Succint data structure library (SDSL). Version 3 has not yet been published, for now cite SDSL-v2 (above).

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