Citation
=====

.. _citation:

If you used the Rp3 pipeline in your work, please cite:

Vieira de Souza E, L. Bookout A, Barnes CA, Miller B, Machado P, Basso LA, Bizarro CV, Saghatelian A. Rp3: Ribosome profiling-assisted proteogenomics improves coverage and confidence during microprotein discovery. Nature Communications. 2024 Aug 9;15(1):6839.

Additionally, depending on which mode you ran and which parameters you used, cite the appropriate software used during the workflow:

``database`` mode
------------

- Cite the paper that presented GTFtoFasta

  Martinez, T.F., Chu, Q., Donaldson, C., Tan, D., Shokhirev, M.N. and Saghatelian, A., 2020. Accurate annotation of human protein-coding small open reading frames. Nature chemical biology, 16(4), pp.458-468.\

``search`` and ``rescore`` mode
------------
- Cite MSFragger

Kong, A.T., Leprevost, F.V., Avtonomov, D.M., Mellacheruvu, D. and Nesvizhskii, A.I., 2017. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature methods, 14(5), pp.513-520.\

- Cite Percolator

Käll, L., Canterbury, J.D., Weston, J., Noble, W.S. and MacCoss, M.J., 2007. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nature methods, 4(11), pp.923-925.

- If you used the flag ``--MSBooster``, cite MSBooster:

Yang, K.L., Yu, F., Teo, G.C., Li, K., Demichev, V., Ralser, M. and Nesvizhskii, A.I., 2023. MSBooster: improving peptide identification rates using deep learning-based features. Nature Communications, 14(1), p.4539.\

``ribocov`` mode
------------
- Cite STAR

Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M. and Gingeras, T.R., 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), pp.15-21.

- Cite featureCounts

Liao, Y., Smyth, G.K. and Shi, W., 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), pp.923-930.

- Cite samtools

Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M.O., Whitwham, A., Keane, T., McCarthy, S.A., Davies, R.M. and Li, H., 2021. Twelve years of SAMtools and BCFtools. Gigascience, 10(2), p.giab008.