Updated citations to include DOIs

Plant-Food-Research-Open · Oct 9, 2024 · dc7659f · dc7659f
1 parent 21e90d1
commit dc7659f
Show file tree

Hide file tree

Showing 4 changed files with 113 additions and 64 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 1. Now using `${meta.id}_trim` as prefix for `FASTQC` files
 2. Added `monochromeLogs` parameter to suppress warnings
+3. Updated citations to include DOIs
 
 ### `Dependencies`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,95 +10,97 @@
 
 ## Pipeline tools
 
-- py_fasta_validator, [MIT](https://github.com/linsalrob/py_fasta_validator/blob/master/LICENSE)
+- AGAT, [GPL v3](https://github.com/NBISweden/AGAT/blob/master/LICENSE)
 
-  > Edwards, R.A. 2019. fasta_validate: a fast and efficient fasta validator written in pure C. doi: <https://doi.org/10.5281/zenodo.2532044>
+  > Jacques Dainat, Darío Hereñú, Dr. K. D. Murray, Ed Davis, Ivan Ugrin, Kathryn Crouch, LucileSol, Nuno Agostinho, pascal-git, Zachary Zollman, & tayyrov. (2024). NBISweden/AGAT: AGAT-v1.4.1 (v1.4.1). Zenodo. doi: <a href="https://doi.org/10.5281/zenodo.13799920">10.5281/zenodo.13799920</a>
 
-- GenomeTools, [ISC](http://genometools.org/license.html)
+- AUGUSTUS, [Artistic license-1.0](https://github.com/Gaius-Augustus/Augustus/blob/master/src/LICENSE.TXT)
 
-  > Gremme G, Steinbiss S, Kurtz S. 2013. "GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 3, pp. 645-656, May 2013, doi: <https://doi.org/10.1109/TCBB.2013.68>
+  > Sommerfeld, D., Lingner, T., Stanke, M., Morgenstern, B., & Richter, H. (2009). AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis. Future Gener. Comput. Syst., 25, 337-345. doi: <a href="https://doi.org/10.1016/j.future.2008.05.010">10.1016/j.future.2008.05.010</a>
 
-- SAMTOOLS, [MIT/Expat](https://github.com/samtools/samtools/blob/develop/LICENSE)
+- BRAKER3, [Artistic license-1.0](https://github.com/Gaius-Augustus/BRAKER/blob/master/LICENSE.TXT)
 
-  > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, <https://doi.org/10.1093/gigascience/giab008>
+  > Gabriel, L., Bruna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M., Stanke, M. (2023). BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA. bioRxiV, doi: <a href="https://doi.org/10.1101/2023.06.10.544449">10.1101/2023.06.10.544449</a>
 
 - BUSCO, [MIT](https://gitlab.com/ezlab/busco/-/blob/master/LICENSE)
 
-  > Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. 2021. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes, Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654, <https://doi.org/10.1093/molbev/msab199>
+  > Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. 2021. BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes, Molecular Biology and Evolution, Volume 38, Issue 10, October 2021, Pages 4647–4654, doi: <a href="https://doi.org/10.1093/molbev/msab199">10.1093/molbev/msab199</a>
 
-- GffRead, [MIT](https://github.com/gpertea/gffread/blob/master/LICENSE)
+- EDTA, [GPL v3](https://github.com/oushujun/EDTA/blob/master/LICENSE)
 
-  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: <http://doi.org/10.12688/f1000research.23297.2>. PMID: 32489650; PMCID: PMC7222033.
+  > Ou S., Su W., Liao Y., Chougule K., Agda J. R. A., Hellinga A. J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N., Hirsch C. N. and Hufford M. B. (2019). Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol. 20(1): 275. doi: <a href="https://doi.org/10.1186/s13059-019-1905-y">10.1186/s13059-019-1905-y</a>
 
-- SEQKIT, [MIT](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
+- EggNOG-mapper, [GPL v3](https://github.com/eggnogdb/eggnog-mapper/blob/master/LICENSE.txt)
 
-  > Shen W, Le S, Li Y, Hu F. 2016. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE 11(10): e0163962. <https://doi.org/10.1371/journal.pone.0163962>
+  > eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. Molecular Biology and Evolution, msab293, doi: <a href="https://doi.org/10.1093/molbev/msab293">10.1093/molbev/msab293</a>
 
-- FASTP, [MIT](https://github.com/OpenGene/fastp/blob/master/LICENSE)
+- FASTQC, [GPL v3](https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt)
 
-  > Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890, <https://doi.org/10.1093/bioinformatics/bty560>
+  > Andrews, S. (2010). Babraham Bioinformatics - FastQC a quality control tool for high throughput sequence data. Babraham.ac.uk. url: <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc">https://www.bioinformatics.babraham.ac.uk/projects/fastqc</a>
 
-- FASTQC, [GPL v3](https://github.com/s-andrews/FastQC/blob/master/LICENSE.txt)
+- FASTP, [MIT](https://github.com/OpenGene/fastp/blob/master/LICENSE)
 
-  > <https://github.com/s-andrews/FastQC>
+  > Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 01 September 2018, Pages i884–i890, doi: <a href="https://doi.org/10.1093/bioinformatics/bty560">10.1093/bioinformatics/bty560</a>
 
-- AGAT, [GPL v3](https://github.com/NBISweden/AGAT/blob/master/LICENSE)
+- GeneMark-ETP, [Attribution-NonCommercial-ShareAlike 4.0 International](https://github.com/gatech-genemark/GeneMark-ETP/blob/main/License-Creative-Commons-Attribution-NonCommercial-ShareAlike-4.0-International.txt)
 
-  > Jacques Dainat, Darío Hereñú, Dr. K. D. Murray, Ed Davis, Ivan Ugrin, Kathryn Crouch, LucileSol, Nuno Agostinho, pascal-git, Zachary Zollman, & tayyrov. (2024). NBISweden/AGAT: AGAT-v1.4.1 (v1.4.1). Zenodo. https://doi.org/10.5281/zenodo.13799920
+  > Brůna T, Lomsadze A, Borodovsky M. GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes. Genome Res. 2024 Jun 25;34(5):757-768. doi: <a href="https://doi.org/10.1101/gr.278373.123">10.1101/gr.278373.123</a>. PMID: 38866548; PMCID: PMC11216313.
 
-- BRAKER, [Artistic license-1.0](https://github.com/Gaius-Augustus/BRAKER/blob/master/LICENSE.TXT)
+- GenomeTools, [ISC](http://genometools.org/license.html)
 
-  > Stanke, M., Diekhans, M., Baertsch, R. and Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, doi: 10.1093/bioinformatics/btn013.
+  > Gremme G, Steinbiss S, Kurtz S. 2013. "GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 3, pp. 645-656, May 2013, doi: <a href="https://doi.org/10.1109/TCBB.2013.68">10.1109/TCBB.2013.68</a>
 
-  > Stanke. M., Schöffmann, O., Morgenstern, B. and Waack, S. (2006). Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7, 62.
+- GffCompare, [MIT](https://github.com/gpertea/gffcompare/blob/master/LICENSE)
 
-  > Gabriel, L., Bruna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M., Stanke, M. (2023). BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA. bioRxiV, doi: 10.1101/2023.06.10.544449.
+  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: <a href="http://doi.org/10.12688/f1000research.23297.2">10.12688/f1000research.23297.2</a>. PMID: 32489650; PMCID: PMC7222033.
 
-  > Bruna, T., Lomsadze, A., Borodovsky, M. (2023). GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistence with Extrinsic Data. bioRxiv, doi: 10.1101/2023.01.13.524024.
+- GffRead, [MIT](https://github.com/gpertea/gffread/blob/master/LICENSE)
 
-  > Kovaka, S., Zimin, A. V., Pertea, G. M., Razaghi, R., Salzberg, S. L., & Pertea, M. (2019). Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome biology, 20(1):1-13.
+  > Pertea G, Pertea M. GFF Utilities: GffRead and GffCompare. F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: <a href="http://doi.org/10.12688/f1000research.23297.2">10.12688/f1000research.23297.2</a>. PMID: 32489650; PMCID: PMC7222033.
 
-- EDTA, [GPL v3](https://github.com/oushujun/EDTA/blob/master/LICENSE)
+- Liftoff, [GPL v3](https://github.com/agshumate/Liftoff/blob/master/LICENSE.md)
 
-  > Ou S., Su W., Liao Y., Chougule K., Agda J. R. A., Hellinga A. J., Lugo C. S. B., Elliott T. A., Ware D., Peterson T., Jiang N., Hirsch C. N. and Hufford M. B. (2019). Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol. 20(1): 275. doi: <https://doi.org/10.1186/s13059-019-1905-y>
+  > Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics. 2021 Jul 19;37(12):1639-1643. doi: <a href="http://doi.org/10.1093/bioinformatics/btaa1016">10.1093/bioinformatics/btaa1016</a>. PMID: 33320174; PMCID: PMC8289374.
 
-- RepeatMasker, [Open Software License v. 2.1](https://github.com/rmhubley/RepeatMasker/blob/master/LICENSE)
+- OrthoFinder, [GPL v3](https://github.com/davidemms/OrthoFinder/blob/master/License.md)
 
-  > <https://github.com/rmhubley/RepeatMasker>
+  > Emms, D.M., Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20, 238 (2019). doi: <a href="https://doi.org/10.1186/s13059-019-1832-y">10.1186/s13059-019-1832-y</a>
 
-- EggNOG-mapper, [GPL v3](https://github.com/eggnogdb/eggnog-mapper/blob/master/LICENSE.txt)
+- ProtHint, [License for GeneMark family software ("Product")](https://github.com/gatech-genemark/ProtHint/blob/master/LICENSE)
+
+  > Tomáš Brůna, Alexandre Lomsadze, Mark Borodovsky, GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins, NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa026, doi: <a href="https://doi.org/10.1093/nargab/lqaa026">10.1093/nargab/lqaa026</a>
 
-  > eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. Molecular Biology and Evolution, msab293, <https://doi.org/10.1093/molbev/msab293>
+- py_fasta_validator, [MIT](https://github.com/linsalrob/py_fasta_validator/blob/master/LICENSE)
 
-  > eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085
+  > Edwards, R.A. 2019. fasta_validate: a fast and efficient fasta validator written in pure C. doi: <a href="https://doi.org/10.5281/zenodo.2532044">10.5281/zenodo.2532044</a>
 
-  > Sensitive protein alignments at tree-of-life scale using DIAMOND. Buchfink B, Reuter K, Drost HG. 2021. Nature Methods 18, 366–368 (2021). <https://doi.org/10.1038/s41592-021-01101-x>
+- RepeatMasker, [Open Software License v. 2.1](https://github.com/rmhubley/RepeatMasker/blob/master/LICENSE)
 
-- Liftoff, [GPL v3](https://github.com/agshumate/Liftoff/blob/master/LICENSE.md)
+  > Smit, A., & Hubley, R. (2023). RepeatMasker: a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Repeatmasker.org. url: <a href="https://www.repeatmasker.org">https://www.repeatmasker.org</a>
 
-  > Shumate, Alaina, and Steven L. Salzberg. 2020. “Liftoff: Accurate Mapping of Gene Annotations.” Bioinformatics , December. <https://doi.org/10.1093/bioinformatics/btaa1016.>
+- RepeatModeler, [Open Software License v. 2.1](https://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSE)
 
-- OrthoFinder, [GPL v3](https://github.com/davidemms/OrthoFinder/blob/master/License.md)
+  > Hubley, R. (2023). RepeatModeler: a de novo transposable element (TE) family identification and modeling package. Repeatmasker.org. url: <a href="https://www.repeatmasker.org">https://www.repeatmasker.org</a>
 
-  > Emms, D.M. and Kelly, S. (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238
+- Samtools, [MIT/Expat](https://github.com/samtools/samtools/blob/develop/LICENSE)
 
-  > Emms, D.M. and Kelly, S. (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16:157
+  > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools, GigaScience, Volume 10, Issue 2, February 2021, giab008, doi: <a href="https://doi.org/10.1093/gigascience/giab008">10.1093/gigascience/giab008</a>
 
-- RepeatModeler, [Open Software License v. 2.1](https://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSE)
+- SeqKit, [MIT](https://github.com/shenwei356/seqkit/blob/master/LICENSE)
 
-  > <https://github.com/Dfam-consortium/RepeatModeler>
+  > Shen W, Le S, Li Y, Hu F. 2016. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE 11(10): e0163962. doi: <a href="https://doi.org/10.1371/journal.pone.0163962">10.1371/journal.pone.0163962</a>
 
-- sortmerna, [GPL v3](https://github.com/sortmerna/sortmerna/blob/master/LICENSE.txt)
+- SortMeRNA, [GPL v3](https://github.com/sortmerna/sortmerna/blob/master/LICENSE.txt)
 
-  > Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: <https://doi.org/10.1093/bioinformatics/bts611>.
+  > Kopylova E., Noé L. and Touzet H., "SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: <a href="https://doi.org/10.1093/bioinformatics/bts611">10.1093/bioinformatics/bts611</a>
 
 - STAR, [MIT](https://github.com/alexdobin/STAR/blob/master/LICENSE)
 
-  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: <https://doi.org/10.1093/bioinformatics/bts635>. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905.
+  > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: <a href="https://doi.org/10.1093/bioinformatics/bts635">10.1093/bioinformatics/bts635</a>. Epub 2012 Oct 25. PMID: 23104886; PMCID: PMC3530905.
 
 - TSEBRA, [The Artistic License 2.0](https://github.com/Gaius-Augustus/TSEBRA/blob/main/bin/LICENSE.txt)
 
-  > Gabriel, L., Hoff, K.J., Brůna, T. et al. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22, 566 (2021). <https://doi.org/10.1186/s12859-021-04482-0>
+  > Gabriel, L., Hoff, K.J., Brůna, T. et al. TSEBRA: transcript selector for BRAKER. BMC Bioinformatics 22, 566 (2021). doi: <a href="https://doi.org/10.1186/s12859-021-04482-0">10.1186/s12859-021-04482-0</a>
 
 ## Software packaging/containerisation tools