SNPest statistics

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Citations per year

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

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

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Popular tool citations

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SNPest specifications

Information


Unique identifier OMICS_08845
Name SNPest
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data SNPest takes input generated by the “samtools mpileup -s” command (or equivalent) reporting nucleotides mapped to each position together with read qualities and mapping qualities.
Output data The output is in VCF format with a line per position covered in the genome.
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Stinus Lindgreen

Publications for SNPest

SNPest citations

 (2)
library_books

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts

2017
mSystems
PMCID: 5686521
PMID: 29152586
DOI: 10.1128/mSystems.00127-17

[…] tie2 with default parameters (). The BAM files were processed using SAMtools (-q 25 -Q 0) to generate mpileup output (). This output was used to create high-confidence genotypes for each strain using SNPest v. 1.0 (minimum depth of 10 reads, minimum posterior probability of 0.999, minimum support for indel of 90%) (). The reference EMBL file was processed using an in-house script to extract all co […]

library_books

Toward high resolution population genomics using archaeological samples

2016
PMCID: 4991838
PMID: 27436340
DOI: 10.1093/dnares/dsw029

[…] ome or only for mtDNA. Such algorithms report the probabilities of different types of postmortem DNA degradation, which allows for better statistical modelling at the variant calling stage, employing SNPest or custom scripts. A typical NGS pipeline for aDNA analysis is shown in . Figure 3. The amount of extracted endogenous DNA may allow satisfactory coverage of aDNA sequences (as high as 10–20x c […]


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SNPest institution(s)
Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Ole Maaloes Vej, Copenhagen, Denmark

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