.. _third party tools:

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