Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

By Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, B. Barnes, F. Schlesinger, Morten Källberg, Anthony J. Cox, S. Kruglyak, Christopher T. Saunders. Bioinform., 2016

1,944 citations recorded by the source corpus.

Subfields: Cancer Research, Genetics

View Paper: https://www.semanticscholar.org/paper/67b3b239ce0cd78664c8458dd2d26fb996c5c972

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Citations in the corpus

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma (2019, methodology): “Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.”
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. (2018, neutral): “1.1 Chen et al., 2016 https://github.com/Illumina/manta Canvas v1.”
Structural variant calling: the long and the short of it (2019, methodology): “Currently, only few methods exist that offer an initial assessment (e.g., Manta [49]).”
VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research (2016, background): “VarDict has similar sensitivity to Lumpy and higher than Manta, although Manta has higher specificity for DEL and DUP.”
Accurate detection of complex structural variations using single molecule sequencing (2017, positive): “With average read lengths of 10kbp or higher, the reads can be more confidently aligned to repetitive sequences that often mediate the formation of SVs 22 .”
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing (2019, neutral): “BreakSeek, BreakSeq2, CLEVER, CREST, DELLY, FermiKit, GASVPro [67], GRIDSS, inGAP-sv, laSV [68], Lumpy, Manta, PBHoney-NGM, pbsv, PRISM [69], SvABA, SVseq2, and Wham provided higher accuracy ( 100-bp RMSV) for lengths of called DELs and/or DUPs, and most of these algorithms used the read pair-based”
A Patient-Derived Glioblastoma Organoid Model and Biobank Recapitulates Inter- and Intra-tumoral Heterogeneity. (2019, methodology): “Prior to running Strelka2, Manta was used to call candidate somatic indels in exome mode across only the primary GRCh38 contigs (Chen et al., 2016).”
Best practices for variant calling in clinical sequencing (2020, methodology): “Structural variants DELLY [51], Lumpy [52], Manta [53], Pindel [54], SVMerge [55]”
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly (2017, methodology): “Some methods apply targeted assembly to validate the breakpoint calls (e.g., Manta [Chen et al. 2016], SVMerge [Wong et al. 2010], TIGRA [Chen et al. 2014]).”