HaploGrep statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HaploGrep
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Tool usage distribution map

This map represents all the scientific publications referring to HaploGrep per scientific context
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Associated diseases

This word cloud represents HaploGrep usage per disease context
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Popular tool citations

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Protocols

HaploGrep specifications

Information


Unique identifier OMICS_07994
Name HaploGrep
Alternative name HaploGrep2
Interface Web user interface, Application programming interface
Restrictions to use None
Input format VCF
Output data An overview of the classification results.
Programming languages Java
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Hansi Weissensteiner

Additional information


http://haplogrep.uibk.ac.at/faq.html

Information


Unique identifier OMICS_07994
Name HaploGrep
Alternative name HaploGrep2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.1.1
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


No version available

Maintainer


  • person_outline Hansi Weissensteiner

Additional information


http://haplogrep.uibk.ac.at/faq.html

Publications for HaploGrep

HaploGrep citations

 (122)
library_books

Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

2018
Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] I (253 bp). For a random subset of 27 samples, new aDNA extracts were generated and used for a replication. In these cases, the haplogroup classification was confirmed. Haplogroups were assigned with Haplogrep 2.0 (http://haplogrep.uibk.ac.at/). Haplogroups showing a quality score below 100% were manually re-evaluated by consulting the established mtDNA phylogeny (www.phylotree.org). […]

library_books

Disclosing the functional changes of two genetic alterations in a patient with Chronic Progressive External Ophthalmoplegia: Report of the novel mtDNA m.7486G>A variant

2018
PMCID: 5952895
PMID: 29398297
DOI: 10.1016/j.nmd.2017.11.006

[…] ble tissues, enriched by a single amplicon long-range PCR followed by massively parallel sequencing , using the HiSeq2000 platform (Illumina technology).Haplogroup of patient was determined using the Haplogrep® tool . […]

library_books

Maternal DNA lineages at the gate of Europe in the 10th century AD

2018
PLoS One
PMCID: 5851556
PMID: 29538439
DOI: 10.1371/journal.pone.0193578

[…] e 57–357) mutational motifs and coding region polymorphic positions were inferred by comparison to the revised Cambridge Reference Sequence (rCRS: NC_012920.1) []. Haplogroups were assigned using the HaploGrep2 web application, based on PhyloTree built 17 [, ]. […]

call_split

Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

2018
PLoS One
PMCID: 5844571
PMID: 29522562
DOI: 10.1371/journal.pone.0194223
call_split See protocol

[…] SNPs. Variants and automated indel calls were manually/visually confirmed directly from the sequences and corrected to avoid alignment errors. SNPs were identified and haplogroups were assigned using Haplogrep 2.0 (http://haplogrep.uibk.ac.at/) [] with the assistance of Mitomap (http://www.mitomap.org/MITOMAP) [] and PhyloTree (http://www.Phylotree.org) []. […]

library_books

Biological Sexing of a 4000 Year Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

2018
Genes
PMCID: 5867856
PMID: 29494531
DOI: 10.3390/genes9030135

[…] ng the number of human sequences observed in the extraction (RB) and library preparation control (NC) samples. The mtDNA haplogroup of the final profile was determined using Phylotree build 17 [] and HaploGrep 2.0 []. Finally, the sequence was compared to other mtDNA sequences from modern and ancient populations stored in GenBank, the European Nucleotide Archives database of the EMBL (ENA) and EMP […]

call_split

Ancient pathogen DNA in human teeth and petrous bones

2018
Ecol Evol
PMCID: 5869295
PMID: 29607044
DOI: 10.1002/ece3.3924
call_split See protocol

[…] of 20 and sites with a sequencing depth of at least 5×, and at each position, a base was called only if it was observed in at least 70% of the reads covering that site (Malaspinas et al., ). We used haplogrep to assign mitochondrial haplogroups of the ancient plague‐positive individuals (Kloss‐Brandstätter et al., ). […]


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HaploGrep institution(s)
Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria; Department of Database and Information Systems, Institute of Computer Science, University of Innsbruck, Innsbruck;, Austria; Department of Mathematics, University of Hamburg, Hamburg, Germany; Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Grupo de Medicina Xenómica (GMX), Facultade de Medicina, Universidade de Santiago de Compostela, Calle San Francisco s/n, Galicia, Spain
HaploGrep funding source(s)
The project was supported by the Austrian Cancer Society/Tirol and by the Tyrolean Science Fund (Tiroler Wissenschaftsfonds).

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