Third party tools
Here is a list of all tools that are integrated into Urgap with proper citations:
- Bowtie
Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https://doi.org/10.1186/gb-2009-10-3-r25
- BowtieBuild
Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). https://doi.org/10.1186/gb-2009-10-3-r25
- CompressToTar
Urgap team (2022)
- CompressToZip
Urgap team (2022)
- CutAdapt
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12. doi:https://doi.org/10.14806/ej.17.1.200
- FastQC
Babraham Bioinformatics group. https://www.bioinformatics.babraham.ac.uk/publications.html
- FilterTabularToCSV
Urgap team (2021)
- FilterTabularToParquet
Urgap team (2021)
- FilterTabularToXlsx
Urgap team (2021)
- KallistoIndex
NL Bray, H Pimentel, P Melsted and L Pachter, Near optimal probabilistic RNA-seq quantification. Nature Biotechnology 34, p 525–527 (2016).
- KallistoQuant
NL Bray, H Pimentel, P Melsted and L Pachter, Near optimal probabilistic RNA-seq quantification. Nature Biotechnology 34, p 525–527 (2016).
- PlinkFreq
Christopher C Chang, Carson C Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun M Purcell, James J Lee, Second-generation PLINK: rising to the challenge of larger and richer datasets, GigaScience, Volume 4, Issue 1, December 2015, s13742-015-0047-8, https://doi.org/10.1186/s13742-015-0047-8
- PlotlyVisualizer
Urgap team 2025
- RpCodonMetrics
Urgap team (2023)
- SamtoolsBamToSam
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. In Bioinformatics (Vol. 25, Issue 16, pp. 2078-2079). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btp352
- SamtoolsIndexBam
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. In Bioinformatics (Vol. 25, Issue 16, pp. 2078-2079). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btp352
- SamtoolsSamToBam
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. In Bioinformatics (Vol. 25, Issue 16, pp. 2078-2079). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btp352
- SamtoolsSortBam
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. In Bioinformatics (Vol. 25, Issue 16, pp. 2078-2079). Oxford University Press (OUP). https://doi.org/10.1093/bioinformatics/btp352
- Star
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England), 29(1), 15-21. https://doi.org/10.1093/bioinformatics/bts635
- StarIndex
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England), 29(1), 15-21. https://doi.org/10.1093/bioinformatics/bts635
- UmiToolsDedup
Smith, T., Heger, A., & Sudbery, I. (2017). UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. In Genome Research (Vol. 27, Issue 3, pp. 491-499). Cold Spring Harbor Laboratory. https://doi.org/10.1101/gr.209601.116
- UmiToolsExtract
Smith, T., Heger, A., & Sudbery, I. (2017). UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. In Genome Research (Vol. 27, Issue 3, pp. 491-499). Cold Spring Harbor Laboratory. https://doi.org/10.1101/gr.209601.116
- VennDiagram
Urgap team 2025