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Bioinformatics. 2017 Dec 1;33(23):3802-3804. doi: 10.1093/bioinformatics/btx423.

GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data.

Author information

1
CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
2
Hematology Department and HCT Unit, G. Papanicolaou Hospital.
3
Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece.
4
Division of Molecular Oncology, Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Università Vita-Salute San Raffaele, Milan, Italy.
5
Department of Internal Medicine--Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.

Abstract

Motivation:

Sanger sequencing is still being employed for sequence variant detection by many laboratories, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases, considerable expertise.

Results:

We present GLASS, a web-based Sanger sequence trace viewer, editor, aligner and variant caller, built to assist with the assessment of variations in 'curated' or user-provided genes. Critically, it produces a standardized variant output as recommended by the Human Genome Variation Society.

Availability and implementation:

GLASS is freely available at http://bat.infspire.org/genomepd/glass/ with source code at https://github.com/infspiredBAT/GLASS.

Contact:

nikos.darzentas@gmail.com or malcikova.jitka@fnbrno.cz.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
29036643
DOI:
10.1093/bioinformatics/btx423
[Indexed for MEDLINE]

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