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Socrates specifications

Information


Unique identifier OMICS_02200
Name Socrates
Alternative name SOft Clip re-alignment To idEntify Structural variants
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0, GNU General Public License version 3.0, MIT License
Computer skills Advanced
Version 1.13.1
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Anthony Papenfuss
  • person_outline Socrates Team

Publication for SOft Clip re-alignment To idEntify Structural variants

Socrates citations

 (6)
library_books

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

2018
Nat Commun
PMCID: 5826927
PMID: 29483503
DOI: 10.1038/s41467-018-03273-1

[…] ping paired-end reads (e.g., VariationHunter, and HYDRA which report only the rough loci of structural variants but not their sequence content); detection of variants using split-read mappings (e.g., Socrates); and detection of variants by mapping de novo assembled contigs to a reference genome (e.g., Barnacle and Dissect, which are RNA-Seq analysis tools that can also be used to analyze genomic d […]

library_books

Genomic characterisation of Eμ Myc mouse lymphomas identifies Bcor as a Myc co operative tumour suppressor gene

2017
Nat Commun
PMCID: 5343491
PMID: 28262675
DOI: 10.1038/ncomms14581

[…] RCm38/mm10). Duplicates were identified and removed from the aligned data using Picard's Mark Duplicates v1.89 (Broad Institute, Boston, MA, USA). BreakDancer v1.3.5 (ref. ), CREST v0.0.1 (ref. ) and Socrates v0.9.5 (ref. ) were employed to identify structural variants. Whole genome de novo assembly was undertaken using Gossamer to compare resulting contigs with the genomic sequence relevant to th […]

call_split

RAG2 and XLF/Cernunnos interplay reveals a novel role for the RAG complex in DNA repair

2016
Nat Commun
PMCID: 4740868
PMID: 26833222
DOI: 10.1038/ncomms10529
call_split See protocol

[…] er and simple repeats tracks respectively (UCSC). The overlap with repeats was computed with BEDTools. Circos plot was used to visualize chromosomal rearrangements and copy number variations. We used Socrates and Delly version 0.5.6 to identify breakpoints of SVs with single-nucleotide resolution and Socrates to predict micro-homologies and untemplated sequences at breakpoints.Copy number variants […]

library_books

Expression of a Chimeric Antigen Receptor in Multiple Leukocyte Lineages in Transgenic Mice

2015
PLoS One
PMCID: 4624721
PMID: 26505904
DOI: 10.1371/journal.pone.0140543

[…] 7292241. To derive the exact transgene sequence, we first looked for aberrations in the mappings around those blocks of homology within the native mouse reference. Structural variation detection with Socrates ([]) detected a total of 86 breakpoints in the sequencing data for F9 () and 69 for F38 (). The breakpoints identified how the transgene components are connected, as well as sub-blocks within […]

library_books

Embryonic Lethality in Homozygous Human Her 2 Transgenic Mice Due to Disruption of the Pds5b Gene

2015
PLoS One
PMCID: 4559457
PMID: 26334628
DOI: 10.1371/journal.pone.0136817

[…] the following steps. The next step was to detect the insertion point(s) of the transgenic material into the native DNA of the mice. We performed structural variation analysis on the alignments using Socrates [] and used Control-FREEC (version 6.7 []) for genome wide copy number analysis to establish the number of transgene instances inserted into the DNA.The breakpoint detection performed with So […]

library_books

Detection of Genomic Structural Variants from Next Generation Sequencing Data

2015
Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] aracterized within the insert size (Karakoc et al., ). Splitread is suitable for WGS/WES reads aligned using mrsFAST (Hach et al., ) to discover indels, SVs, de novo events, and pseudogenes.Recently, Socrates (a SR method designed for cancer genomics) was compared to several tools (Schröder et al., ), including BreakDancer, CLEVER, CREST (Wang et al., ), DELLY (Rausch et al., ), Pindel, and PRISM […]

Citations

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Socrates institution(s)
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, VIC, Australia; Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Department of Pathology, The University of Melbourne, VIC, Australia; NICTA Victoria Laboratory, The University of Melbourne, VIC, Australia; Department of Computing and Information Systems, University of Melbourne, VIC, Australia; Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, VIC, Australia; Department of Mathematics and Statistics, The University of Melbourne, VIC, Australia; Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
Socrates funding source(s)
Supported by a National Health and Medical Research Council (NHMRC) Project Grant (637357), Victorian State Government Operational Infrastructure Support, Australian Government NHMRC IRIISS, the Melbourne Melanoma Project, the Victorian Cancer Biobank and the Victorian Cancer Agency, a Cancer Council of Victoria scholarship, NICTA funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council through the ICT Centre of Excellence program, NHMRC Principal Research Fellowship, The Cancer Council Victoria, The Leukaemia Foundation of Australia and the Victorian Cancer Agency, fellowships from Pfizer Australia and VESKI, an NHMRC Career Development Fellowship (1003856) and The Lorenzo and Pamela Galli Melanoma Research Fellowship.

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