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Data released on September 22, 2017

Supporting data for "Lightning-fast genome variant detection with GROM"

Grigoriev, A; Kawash, J, K; Smith, S, D (2017): Supporting data for "Lightning-fast genome variant detection with GROM" GigaScience Database. http://dx.doi.org/10.5524/100352 RIS BibTeX Text

Current human whole genome sequencing projects produce massive amounts of data, often creating significant computational challenges. Different approaches have been developed for each type of genome variant and method of its detection, necessitating users to run multiple algorithms to find variants.
We present GROM (Genome Rearrangement OmniMapper), a novel comprehensive variant detection algorithm accepting aligned read files as input and finding SNVs, indels, structural variants (SVs), and copy number variants (CNVs). We show that GROM outperforms state-of-the-art methods on seven validated benchmarks using two whole genome sequencing (WGS) datasets. Additionally, GROM boasts lightning fast run times, analyzing a 50x WGS human dataset (NA12878) on commonly available computer hardware in 11 minutes, more than an order of magnitude (up to 72 times) faster than tools detecting a similar range of variants.
Addressing the needs of big data analysis, GROM combines in one algorithm SNV, indel, SV, and CNV detection providing superior speed, sensitivity, and precision.

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Related manuscripts:

doi:10.1093/gigascience/gix091

Additional information:

http://doi.org/10.17605/OSF.IO/6RTWS

Keywords:

variant detection grom snvs structural variants indels copy number variants whole genome sequencing 

Software

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Funding:

  • Funding body - National Science Foundation
  • Award ID - DBI-1458202
  • Awardee - A. Grigoriev

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Sequence variantsVCF3.27 KB2017-09-13
Sequence variantsVCF2.77 MB2017-09-13
AlignmentsBAM12.57 MB2017-09-13
AlignmentsBAM51.19 KB2017-09-13
Displaying 11-14 of 14 File(s).

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