sv-gen
SV
Highly portable parallel workflow to generate artificial genomes with structural variants.
Updated 33 months ago
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sv-callers
Highly portable parallel workflow to detect structural variants in cancer genomes.
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contributors
Cite this software
Description
- Enables comprehensive detection of structural variants (SVs) by combining multiple tools
- Supports both single-sample (germline) and paired-sample (somatic) SV analyses
- Makes the analyses scalable and easily portable across HPC clusters (e.g., using GridEngine, Slurm etc.) or compute clouds
- It's easy to use, deploy and extend with new tools
This Snakemake-based workflow combines several state-of-the-art tools (i.e. Manta, DELLY, LUMPY and GRIDSS) for detecting structural variants (SVs) in whole genome sequencing data. The workflow is easy to use and to deploy on any Linux-based machine. In particular, the workflow supports automated software deployment, easy configuration and addition of new analysis tools as well as enables to scale from a single computer to different HPC clusters with minimal effort.
License
Participating organisations
Reference papers
Mentions
Portable HPC workflows with Snakemake, Conda, and Xenon
Author(s): Jurriaan H. Spaaks
Published in 2018
Journal articles
12- 1.Author(s): David E. Torres, H. Martin Kramer, Vittorio Tracanna, Gabriel L. Fiorin, David E. Cook, Michael F. Seidl, Bart P. H. J. ThommaPublished in Nature Communications by Springer Science and Business Media LLC in 202410.1038/s41467-024-45884-x
- 2.Author(s): Jennifer D. Yuzon, Zachary Schultzhaus, Zheng WangPublished in Microbiology Spectrum by American Society for Microbiology in 202310.1128/spectrum.02219-23
- 3.Author(s): Markus Schmidt, Arne KutznerPublished in Genome Biology by Springer Science and Business Media LLC in 202310.1186/s13059-023-03009-5
- 4.Author(s): Tatiana Maroilley, K M Tahsin Hassan Rahit, Afiya Razia Chida, Filip Cotra, Victoria Rodrigues Alves Barbosa, Maja Tarailo-GraovacPublished in G3: Genes, Genomes, Genetics by Oxford University Press (OUP) in 202310.1093/g3journal/jkad184
- 5.Author(s): Yu Lei, Yue Meng, Xinqi Guo, Ke Ning, Yixin Bian, Lanlan Li, Zhenduo Hu, Anastasia A. Anashkina, Qinghua Jiang, Yucui Dong, Xiao ZhuPublished in Computers in Biology and Medicine by Elsevier BV in 2022, page: 10553410.1016/j.compbiomed.2022.105534
- 6.Author(s): David E Torres, Bart P H J Thomma, Michael F SeidlPublished in Genome Biology and Evolution by Oxford University Press (OUP) in 202110.1093/gbe/evab135
- 7.Author(s): Shane C. Campbell-Staton, Brian J. Arnold, Dominique Gonçalves, Petter Granli, Joyce Poole, Ryan A. Long, Robert M. PringlePublished in Science by American Association for the Advancement of Science (AAAS) in 2021, page: 483-48710.1126/science.abe7389
- 8.Author(s): Itsuki Sugita, Shohei Matsuyama, Hiroki Dobashi, Daisuke Komura, Shumpei IshikawaPublished in Bioinformatics by Oxford University Press (OUP) in 2021, page: 540-54210.1093/bioinformatics/btab662
- 9.Author(s): Rena M Schweizer, Norah Saarman, Kristina M Ramstad, Brenna R Forester, Joanna L Kelley, Brian K Hand, Rachel L Malison, Amanda S Ackiss, Mrinalini Watsa, Thomas C Nelson, Albano Beja-Pereira, Robin S Waples, W Chris Funk, Gordon LuikartPublished in Journal of Heredity by Oxford University Press (OUP) in 2021, page: 313-32710.1093/jhered/esab019
- 10.Author(s): Ksenia Lavrichenko, Stefan Johansson, Inge JonassenPublished in BMC Genomics by Springer Science and Business Media LLC in 202110.1186/s12864-021-08082-3
- 11.Author(s): Arnold Kuzniar, Jason Maassen, Stefan Verhoeven, Luca Santuari, Carl Shneider, Wigard P. Kloosterman, Jeroen de RidderPublished in PeerJ by PeerJ in 2020, page: e821410.7717/peerj.8214
- 12.Author(s): Wesley J. Delage, Julien Thevenon, Claire LemaitrePublished in BMC Genomics by Springer Science and Business Media LLC in 202010.1186/s12864-020-07125-5
Other
11- 1.Author(s): Megan K. Le, Qian Qin, Heng LiPublished by Cold Spring Harbor Laboratory in 202410.1101/2024.07.29.605160
- 2.Author(s): Célian Diblasi, Nicola Barson, Marie SaitouPublished by California Digital Library (CDL) in 202310.32942/x2j59q
- 3.Author(s): David E. Torres, H. Martin Kramer, Vittorio Tracanna, Gabriel L. Fiorin, David E. Cook, Michael F. Seidl, Bart P.H.J. ThommaPublished by Cold Spring Harbor Laboratory in 202310.1101/2023.04.04.535574
- 4.Author(s): David E Torres, Bart PHJ Thomma, Michael F SeidlPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.01.25.428111
- 5.Author(s): Itsuki Sugita, Shohei Matsuyama, Hiroki Dobashi, Daisuke Komura, Shumpei IshikawaPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.03.31.437648
- 6.Author(s): Markus Schmidt, Arne KutznerPublished by Cold Spring Harbor Laboratory in 202110.1101/2021.01.12.426317
- 7.Published by PeerJ in 202010.7287/peerj.8214v0.1/reviews/1
- 8.Author(s): Wesley Delage, Julien Thevenon, Claire LemaitrePublished by Cold Spring Harbor Laboratory in 202010.1101/2020.06.09.142232
- 9.Author(s): C DavisPublished by PeerJ in 202010.7287/peerj.8214v0.2/reviews/3
- 10.Published by PeerJ in 202010.7287/peerj.8214v0.2/reviews/1
- 11.Published by PeerJ in 202010.7287/peerj.8214v0.1/reviews/2
Contributors
Contact person
Arnold Kuzniar
Netherlands eScience Center
LS
Luca Santuari
University Medical Center Utrecht
Netherlands eScience Center
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Googling the cancer genome
Identification and prioritization of cancer-causing structural variations in whole genomes
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