12 References
Andrews, Simon. 2010. “FastQC: A Quality Control Tool for High Throughput Sequence Data.”
Eric Olivier Audemard, Patrick Gendron, Vincent-Philippe Lavallée, Josée Hébert, Guy Sauvageau, Sébastien Lemieux. 2018. “Targeted Variant Detection in Leukemia Using Unaligned RNA-Seq Reads.” bioRXiv, April.
Ewels, Philip, Måns Magnusson, Sverker Lundin, and Max Käller. 2016. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics 32 (19): 3047–8.
Flensburg, Christoffer, Tobias Sargeant, Alicia Oshlack, and Ian Majewski. 2018. “SuperFreq: Integrated Mutation Detection and Clonal Tracking in Cancer.” bioRxiv.
Institute, Broad. n.d. “Picard Tools.” http://broadinstitute.github.io/picard.
Koboldt, Daniel C, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, and Richard K Wilson. 2012. “VarScan 2: Somatic Mutation and Copy Number Alteration Discovery in Cancer by Exome Sequencing.” Genome Res. 22 (3): 568–76.
Lai, Zhongwu, Aleksandra Markovets, Miika Ahdesmaki, Brad Chapman, Oliver Hofmann, Robert McEwen, Justin Johnson, Brian Dougherty, J Carl Barrett, and Jonathan R Dry. 2016. “VarDict: A Novel and Versatile Variant Caller for Next-Generation Sequencing in Cancer Research.” Nucleic Acids Res. 44 (11): e108.
Lavallée, Vincent-Philippe, Sébastien Lemieux, Geneviève Boucher, Patrick Gendron, Isabel Boivin, Richard Neil Armstrong, Guy Sauvageau, and Josée Hébert. 2016. “RNA-sequencing Analysis of Core Binding Factor AML Identifies Recurrent ZBTB7A Mutations and Defines RUNX1-CBFA2T3 Fusion Signature.” Blood, March.
McKenna, Aaron, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, et al. 2010. “The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data.” Genome Res. 20 (9): 1297–1303.
McLaren, William, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, and Fiona Cunningham. 2016. “The Ensembl Variant Effect Predictor.” Genome Biol. 17 (1): 122.
Tange, Ole. n.d. “GNU Parallel: The Command-Line Power Tool.”