.

Author: DaanJansen94

docs/citations/CITATIONS.md

@@ -14,31 +14,31 @@ Jansen, D., & Vercauteren, K. (2026). Virasign: A viral taxonomic classification
 
 ### Docker
 
-Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal. 2014 Mar 1;239:Article 2. doi: [10.5555/2600239.2600241](https://doi.org/10.5555/2600239.2600241).
+Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal. 2014 Mar 1;239:Article 2. doi: https://doi.org/10.5555/2600239.2600241.
 
 ### Singularity
 
-Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: [10.1371/journal.pone.0177459](https://doi.org/10.1371/journal.pone.0177459).
+Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: https://doi.org/10.1371/journal.pone.0177459.
 
 ---
 
 ## Core bioinformatics tools used by Virasign
 
 ### minimap2
 
-Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: [10.1093/bioinformatics/bty191](https://doi.org/10.1093/bioinformatics/bty191).
+Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: https://doi.org/10.1093/bioinformatics/bty191.
 
 ### SAMtools
 
-Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-2079. doi: [10.1093/bioinformatics/btp352](https://doi.org/10.1093/bioinformatics/btp352).
+Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-2079. doi: https://doi.org/10.1093/bioinformatics/btp352.
 
 ### seqtk
 
 Li H. seqtk: Toolkit for processing sequences in FASTA/FASTQ format. https://github.com/lh3/seqtk
 
 ### MMseqs2
 
-Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017 Nov;35(11):1026-1028. doi: [10.1038/nbt.3988](https://doi.org/10.1038/nbt.3988).
+Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017 Nov;35(11):1026-1028. doi: https://doi.org/10.1038/nbt.3988.
 
 ### Nextclade
 
@@ -52,8 +52,8 @@ If you run Virasign as part of a workflow framework, please cite the framework y
 
 ### nf-core
 
-Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: [10.1038/s41587-020-0439-x](https://doi.org/10.1038/s41587-020-0439-x).
+Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: https://doi.org/10.1038/s41587-020-0439-x.
 
 ### Nextflow
 
-Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: [10.1038/nbt.3820](https://doi.org/10.1038/nbt.3820).
+Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: https://doi.org/10.1038/nbt.3820.