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Bioinformatics. 2016 Oct 1;32(19):3021-3. doi: 10.1093/bioinformatics/btw369. Epub 2016 Jun 17.

Assemblytics: a web analytics tool for the detection of variants from an assembly.

Author information

1
Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY, USA and.
2
Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, NY, USA and Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.

Abstract

Assemblytics is a web app for detecting and analyzing variants from a de novo genome assembly aligned to a reference genome. It incorporates a unique anchor filtering approach to increase robustness to repetitive elements, and identifies six classes of variants based on their distinct alignment signatures. Assemblytics can be applied both to comparing aberrant genomes, such as human cancers, to a reference, or to identify differences between related species. Multiple interactive visualizations enable in-depth explorations of the genomic distributions of variants.

AVAILABILITY AND IMPLEMENTATION:

http://assemblytics.com, https://github.com/marianattestad/assemblytics

CONTACT:

mnattest@cshl.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27318204
PMCID:
PMC6191160
DOI:
10.1093/bioinformatics/btw369
[Indexed for MEDLINE]
Free PMC Article

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