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GeneticThesaurus

Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. GeneticThesaurus is a method for quick and robust variant detection in low-mappability regions.

Official website
Specifications
Doc. & support
Credits
Publications
Classification

Specifications

Software type:: Package
Interface:: Command line interface
Restrictions to use:: None
Operating system:: Unix/Linux
Computer skills:: Advanced
Stability:: Stable

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Documentation & support

Maintainer

Tomasz Konopka <tomasz.konopka at ludwig.ox.ac.uk>

Credits

Institution(s)

Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria

Publications

(Kerzendorfer et al., 2015) A thesaurus of genetic variation for interrogation of repetitive genomic regions. Nucleic acids research.
PMID: 25820428

Classification

Literature

(Mainzer et al., 2015) Isaac, the Illumina variant calling workflow. bioRxiv.
DOI: 10.1101/031021
(Liu et al., 2013) Variant callers for next-generation sequencing data: a comparison study. PloS one.
PMID: 24086590
(Nielsen et al., 2011) Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics.
PMID: 21587300
(Altmann et al., 2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Human genetics.
PMID: 22886560
(Pabinger et al., 2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics.
PMID: 23341494
(Yi et al., 2014) Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids research.
PMID: 24831545
(Pirooznia et al., 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human genomics.
PMID: 25078893

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