Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads

Jan SchröderAnthony T Papenfuss


Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates. In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools. Socrates is released as open source and available from CONTACT: Supplementary information: Supplementary data are available at Bioinformatics online.


May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Sep 2, 2010·Genome Research·Paul MedvedevMichael Brudno
Oct 29, 2010·Nature·Peter J CampbellP Andrew Futreal
Feb 10, 2011·PloS One·Christopher A MillerAleksandar Milosavljevic
Jun 1, 2011·PLoS Computational Biology·Andrew McPhersonSohrab P Shah
Oct 14, 2011·Genome Research·Chris D GreenmanPeter J Campbell
Oct 18, 2011·BMC Bioinformatics·Eric C RouchkaRamin Homayouni
Dec 20, 2011·Nature Methods·Emre KarakocEvan E Eichler
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Oct 13, 2012·Bioinformatics·Tobias MarschallAlexander Schönhuth


Feb 3, 2016·Nature Communications·Chloé LescaleLudovic Deriano
Oct 9, 2015·Thrombosis and Haemostasis·Marisa L R CunhaSaskia Middeldorp
Apr 17, 2015·Briefings in Functional Genomics·Geòrgia EscaramísRaquel Rabionet
Feb 28, 2018·Nature Communications·Ibrahim NumanagićS Cenk Sahinalp
Apr 18, 2019·Genome Research·Roven Rommel FuentesNickolai Alexandrov
May 24, 2019·Nature·François BertucciFabrice André
Feb 7, 2020·Nature Communications·Marek CmeroPCAWG Consortium
Mar 28, 2019·Nature Communications·Luigi FormisanoCarlos L Arteaga
Feb 14, 2019·Nucleic Acids Research·Alexander R GawrońskiFaraz Hach
Aug 31, 2019·Genes, Chromosomes & Cancer·Julie HoElizabeth G Demicco
Nov 19, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Iulian GaburIsobel A P Parkin
Aug 28, 2020·Frontiers in Genetics·Jinxin DongXiguo Yuan
Apr 2, 2015·Nature Communications·Matthew K H HongChristopher M Hovens
Jul 22, 2017·BMC Bioinformatics·Jan SchröderAnthony T Papenfuss
Dec 18, 2020·Microbial Genomics·Stephen J Bush
Dec 3, 2015·Cancer Research·Stephen Q WongRichard W Tothill

Related Concepts

Malignant Neoplasms
Computer Programs and Programming
Sequence Determinations, DNA
Computational Molecular Biology
High-Throughput Nucleotide Sequencing
Malignant Neoplasms
Gene Rearrangement

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