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Protocols

schmutzi specifications

Information


Unique identifier OMICS_10291
Name schmutzi
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data text
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++, Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Janet Kelso

Publication for schmutzi

schmutzi citations

 (14)
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

[…] sing Burrows-Wheeler-Aligner (BWA) []; reads with mapping quality below 30 were discarded and PCR duplicates were removed by rmdup in SAMtools []. For all samples, a probabilistic iterative approach, Schmutzi [], was used to call the endogenous consensus sequences and to estimate the contamination levels. Misincorporation patterns were tracked and quantified by mapDamage 2.0 []. The latter one was […]

library_books

Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche

2018
Sci Rep
PMCID: 5794802
PMID: 29391530
DOI: 10.1038/s41598-018-20180-z

[…] hr was determined. For this purpose, a complete 395 X coverage mitochondrial genome of George Bähr was reconstructed and a quality filtered (q > 30) consensus sequence of his genome was created using schmutzi. His maternal haplogroup was determined to be H35 using Haplogrep 2, which is a common subclade of haplogroup H in Central Europe. Furthermore, the Y chromosomal haplogroup of George Bähr was […]

library_books

The genetic prehistory of the Baltic Sea region

2018
Nat Commun
PMCID: 5789860
PMID: 29382937
DOI: 10.1038/s41467-018-02825-9

[…] d from further analyses. We evaluated the authenticity of the samples by observing typical patterns of deamination towards read ends (Supplementary Data ), estimating heterozygosity on the mtDNA with schmutzi and heterozygosity on the X chromosome in male samples with ANGSD (Supplementary Data ), and evaluating the ratio of the reads mapping to X and Y which showed no outliers (see below).We obser […]

library_books

Successful reconstruction of whole mitochondrial genomes from ancient Central America and Mexico

2017
Sci Rep
PMCID: 5741722
PMID: 29273718
DOI: 10.1038/s41598-017-18356-0

[…] on the basis of identical 5′ and 3′ mapping positions (https://bitbucket.org/ustenzel/biohazard). Mapped reads were further filtered to those with a minimum length of 35 bp and minimum quality of 30. Schmutzi was utilized to estimate endogenous mitochondrial consensus sequences and contamination (−qual 10) using the comparative Eurasian database. Automated indel calls were manually confirmed direc […]

call_split

Genetic origins of the Minoans and Mycenaeans

2017
Nature
PMCID: 5565772
PMID: 28783727
DOI: 10.1038/nature23310
call_split See protocol

[…] Modern human contamination of the mitochondrial DNA was assessed using the software schmutzi which takes into account that the consensus sequence should be reconstructed from reads showing characteristics of ancient DNA and originating from a single individual (). We assessed contami […]

call_split

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

2017
Nat Commun
PMCID: 5500885
PMID: 28675384
DOI: 10.1038/ncomms16046
call_split See protocol

[…] fragment length and deamination patterns (). Statistics for each processing step of the four reference sequences are reported in .Consensus reconstruction was performed in a two-step approach. First, schmutzi was used to infer the endogenous sequence. An internal program of the software package (contDeam) was first run to calculate the endogenous deamination rate and a contamination prior. To each […]


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schmutzi institution(s)
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada

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