Tag: Contamination

PMDtools 0.5 – Separating Ancient DNA from Modern Contamination

PMDtools 0.5

:: DESCRIPTION

PMDtools implements a likelihood framework including postmortem damage (PMD), base quality scores and biological polymorphism to allow the identification of degraded DNA sequences that are unlikely to originate from modern contamination.

::DEVELOPER

Jakobsson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  PMDtools

:: MORE INFORMATION

Citation

P Skoglund, BH Northoff, MV Shunkov, A Derevianko, S Pääbo, J Krause, M Jakobsson (2014)
Separating ancient DNA from modern contamination in a Siberian Neandertal,
Proceedings of the National Academy of Sciences USA doi:10.1073/pnas.1318934111

DeconSeq 0.4.3 – Detect and Remove Contaminations from Metagenomic datasets

DeconSeq 0.4.3

:: DESCRIPTION

DeconSeq is a tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length).

DeconSeq Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 DeconSeq

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
PLoS ONE 2011, 6:e17288

BAFRegress 0.9.3 – Detects and Estimates Sample Contamination using B allele frequency data

BAFRegress 0.9.3

:: DESCRIPTION

BAFRegress is a software that detects and estimates sample contamination using B allele frequency data from Illumina genotyping arrays using a regression model.

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 BAFRegress

:: MORE INFORMATION

Citation

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang,
Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data, 
Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. (volume 91 issue 5 pp.839 – 848)

verifyBamID 1.1.3 – Identify Contamination of Sample Swap in Sequence data

verifyBamID 1.1.3

:: DESCRIPTION

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 verifyBamID

:: MORE INFORMATION

Citation

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang,
Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data,
Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. (volume 91 issue 5 pp.839 – 848)