CHURP: A Lightweight CLI Framework to Enable Novice Users to Analyze Sequencing Datasets in Parallel

Enis Afgan, Dannon Baker, Marius van denÂăBeek, Daniel Blankenberg, Dave Bouvier, Martin ÄŇech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, BjÃűrn GrÃijning, Aysam Guerler, Jennifer Hillman-Jackson, Greg Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, and Jeremy Goecks. 2016. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research 44, W1 (July 2016), W3--W10.

J. J. Allaire, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2018. rmarkdown: Dynamic Documents for R. https://rmarkdown.rstudio.com

S Andrews. 2014. FastQC A Quality Control tool for High Throughput Sequence Data.

Anthony M. Bolger, Marc Lohse, and BJoern Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 15 (Aug. 2014), 2114--2120.

Arie B. Brinkman, Femke Simmer, Kelong Ma, Anita Kaan, Jingde Zhu, and Hendrik G. Stunnenberg. 2010. Whole-genome DNA methylation profiling using MethylCap-seq. DNA Methylation Analysis 52, 3 (Nov. 2010), 232--236.

Peter J. Campbell, Philip J. Stephens, Erin D. Pleasance, Sarah O'Meara, Heng Li, Thomas Santarius, Lucy A. Stebbings, Catherine Leroy, Sarah Edkins, Claire Hardy, Jon W. Teague, Andrew Menzies, Ian Goodhead, Daniel J. Turner, Christopher M. Clee, Michael A. Quail, Antony Cox, Clive Brown, Richard Durbin, Matthew E. Hurles, Paul A. W. Edwards, Graham R. Bignell, Michael R. Stratton, and P. Andrew Futreal. 2008. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genetics 40, 6 (June 2008), 722--729.

Murim Choi, Ute I. Scholl, Weizhen Ji, Tiewen Liu, Irina R. Tikhonova, Paul Zumbo, Ahmet Nayir, AyÈŹin Bakkaloħlu, Seza ÃŰzen, Sami Sanjad, Carol Nelson-Williams, Anita Farhi, Shrikant Mane, and Richard P. Lifton. 2009. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences 106, 45 (Nov. 2009), 19096.

DNAStar. (accessed May 17, 2019). DNAStar Genomics Suite. https://www. dnastar.com/software/genomics/

Terrence S. Furey. 2012. ChIPâĂŞseq and beyond: new and improved methodologies to detect and characterize proteinâĂŞDNA interactions. Nature Reviews Genetics 13, 12 (Dec. 2012), 840--852.

Daehwan Kim, Ben Langmead, and Steven L. Salzberg. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12, 4 (April 2015), 357--360.

Jeremy Leipzig. 2017. A review of bioinformatic pipeline frameworks. Briefings in Bioinformatics 18, 3 (May 2017), 530--536.

Joshua Z. Levin, Moran Yassour, Xian Adiconis, Chad Nusbaum, Dawn Anne Thompson, Nir Friedman, Andreas Gnirke, and Aviv Regev. 2010. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature methods 7, 9 (Sept. 2010), 709--715.

Yang Liao, Gordon K. Smyth, and Wei Shi. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics (Oxford, England) 30, 7 (April 2014), 923--930.

Nirav Merchant, Eric Lyons, Stephen Goff, Matthew Vaughn, Doreen Ware, David Micklos, and Parker Antin. 2016. The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences. PLOS Biology 14, 1 (Jan. 2016), e1002342.

Paul Muir, Shantao Li, Shaoke Lou, Daifeng Wang, Daniel J. Spakowicz, Leonidas Salichos, Jing Zhang, George M. Weinstock, Farren Isaacs, Joel Rozowsky, and Mark Gerstein. 2016. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biology 17, 1 (March 2016), 53.

QIAGEN. (accessed May 17, 2019). CLC Genomics Workbench 12.0. https://www.qiagenbioinformatics.com/

R Core Team. 2018. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

Mark D. Robinson, Davis J. McCarthy, and Gordon K. Smyth. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 1 (Jan. 2010), 139--140.

Kris A. Wetterstrand. (accessed May 17, 2019). DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP). https://www.genome.gov/27541954/dna-sequencing-costs-data/

Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, MercÃĺ Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C âĂŹt Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, and Barend Mons. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3 (March 2016).

Chao Xie and Martti T. Tammi. 2009. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10, 1 (March 2009), 80.