References

Meers2019

Meers, Michael P., et al. “Improved CUT&RUN chromatin profiling tools.” Elife 8 (2019): e46314.

Nextflow_Citation

Di Tommaso, Paolo, et al. “Nextflow enables reproducible computational workflows.” Nature biotechnology 35.4 (2017): 316-319.

Bioconda_Citation

Grüning, Björn, et al. “Bioconda: sustainable and comprehensive software distribution for the life sciences.” Nature methods 15.7 (2018): 475-476.

CUTRUNTools_Citation

Zhu, Qian, et al. “CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis.” Genome biology 20.1 (2019): 192.

SEACR_Citation

Meers, Michael P., Dan Tenenbaum, and Steven Henikoff. “Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling.” Epigenetics & chromatin 12.1 (2019): 42.

R_Citation

R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/

BioContainers_Citation

Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber, Mingze Bai, Rafael C Jimenez, Timo Sachsenberg, Julianus Pfeuffer, Roberto Vera Alvarez, Johannes Griss, Alexey I Nesvizhskii, Yasset Perez-Riverol, BioContainers: an open-source and community-driven framework for software standardization, Bioinformatics, Volume 33, Issue 16, 15 August 2017, Pages 2580–2582, https://doi.org/10.1093/bioinformatics/btx192

Bowtie2_Citation

Langmead, Ben, and Steven L. Salzberg. “Fast gapped-read alignment with Bowtie 2.” Nature methods 9.4 (2012): 357.

faCount_Citation

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.

Samtools_Citation

Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

FastQC_Citation

Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Trimmomatic_Citation

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.

bedtools_Citation

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

bedGraphToBigWig_Citation

BigWig and BigBed tools: Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed data sets. Bioinformatics. 2010 Sep 1;26(17):2204-7.

MACS2_Citation

Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137

References (BibTeX)

Download Citations.bib

@article{di2017nextflow,
  title={Nextflow enables reproducible computational workflows},
  author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  journal={Nature biotechnology},
  volume={35},
  number={4},
  pages={316--319},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{gruning2018bioconda,
  title={Bioconda: sustainable and comprehensive software distribution for the life sciences},
  author={Gr{\"u}ning, Bj{\"o}rn and Dale, Ryan and Sj{\"o}din, Andreas and Chapman, Brad A and Rowe, Jillian and Tomkins-Tinch, Christopher H and Valieris, Renan and K{\"o}ster, Johannes},
  journal={Nature methods},
  volume={15},
  number={7},
  pages={475--476},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{zhu2019cut,
  title={CUT\&RUNTools: a flexible pipeline for CUT\&RUN processing and footprint analysis},
  author={Zhu, Qian and Liu, Nan and Orkin, Stuart H and Yuan, Guo-Cheng},
  journal={Genome biology},
  volume={20},
  number={1},
  pages={192},
  year={2019},
  publisher={Springer}
}

@article{meers2019peak,
  title={Peak calling by Sparse Enrichment Analysis for CUT\&RUN chromatin profiling},
  author={Meers, Michael P and Tenenbaum, Dan and Henikoff, Steven},
  journal={Epigenetics \& chromatin},
  volume={12},
  number={1},
  pages={42},
  year={2019},
  publisher={Springer}
}

@Manual{,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2017},
  url = {https://www.R-project.org/},
}

@article{10.1093/bioinformatics/btx192,
    author = {da Veiga Leprevost, Felipe and Grüning, Björn A and Alves Aflitos, Saulo and Röst, Hannes L and Uszkoreit, Julian and Barsnes, Harald and Vaudel, Marc and Moreno, Pablo and Gatto, Laurent and Weber, Jonas and Bai, Mingze and Jimenez, Rafael C and Sachsenberg, Timo and Pfeuffer, Julianus and Vera Alvarez, Roberto and Griss, Johannes and Nesvizhskii, Alexey I and Perez-Riverol, Yasset},
    title = "{BioContainers: an open-source and community-driven framework for software standardization}",
    journal = {Bioinformatics},
    volume = {33},
    number = {16},
    pages = {2580-2582},
    year = {2017},
    month = {03},
    abstract = "{BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters).The software is freely available at github.com/BioContainers/.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btx192},
    url = {https://doi.org/10.1093/bioinformatics/btx192},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/33/16/2580/25163480/btx192.pdf},
}

@article{langmead2012fast,
  title={Fast gapped-read alignment with Bowtie 2},
  author={Langmead, Ben and Salzberg, Steven L},
  journal={Nature methods},
  volume={9},
  number={4},
  pages={357},
  year={2012},
  publisher={Nature Publishing Group}
}

@article{kent2002human,
  title={The human genome browser at UCSC},
  author={Kent, W James and Sugnet, Charles W and Furey, Terrence S and Roskin, Krishna M and Pringle, Tom H and Zahler, Alan M and Haussler, David},
  journal={Genome research},
  volume={12},
  number={6},
  pages={996--1006},
  year={2002},
  publisher={Cold Spring Harbor Lab}
}

@article{li2009sequence,
  title={The sequence alignment/map format and SAMtools},
  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
  journal={Bioinformatics},
  volume={25},
  number={16},
  pages={2078--2079},
  year={2009},
  publisher={Oxford University Press}
}

@misc{andrews2015quality,
  title={A quality control tool for high throughput sequence data. 2010},
  author={Andrews, Simon and FastQC, A},
  year={2015}
}

@article{bolger2014trimmomatic,
  title={Trimmomatic: a flexible trimmer for Illumina sequence data},
  author={Bolger, Anthony M and Lohse, Marc and Usadel, Bjoern},
  journal={Bioinformatics},
  volume={30},
  number={15},
  pages={2114--2120},
  year={2014},
  publisher={Oxford University Press}
}

@article{quinlan2010bedtools,
  title={BEDTools: a flexible suite of utilities for comparing genomic features},
  author={Quinlan, Aaron R and Hall, Ira M},
  journal={Bioinformatics},
  volume={26},
  number={6},
  pages={841--842},
  year={2010},
  publisher={Oxford University Press}
}

@article{kent2010bigwig,
  title={BigWig and BigBed: enabling browsing of large distributed datasets},
  author={Kent, W James and Zweig, Ann S and Barber, G and Hinrichs, Angie S and Karolchik, Donna},
  journal={Bioinformatics},
  volume={26},
  number={17},
  pages={2204--2207},
  year={2010},
  publisher={Oxford University Press}
}

@article{zhang2008model,
  title={Model-based analysis of ChIP-Seq (MACS)},
  author={Zhang, Yong and Liu, Tao and Meyer, Clifford A and Eeckhoute, J{\'e}r{\^o}me and Johnson, David S and Bernstein, Bradley E and Nusbaum, Chad and Myers, Richard M and Brown, Myles and Li, Wei and others},
  journal={Genome biology},
  volume={9},
  number={9},
  pages={1--9},
  year={2008},
  publisher={BioMed Central}
}