BioinformaticsBioinformaticsPeer-reviewed journal article
read_haps: using read haplotypes to detect same species contamination in DNA sequences.
Abstract
MotivationData analysis is requisite on reliable data. In genetics this includes verifying that the sample is not contaminated with another, a problem ubiquitous in biology. ResultsIn human, and other diploid species, DNA contamination from the same species can be found by the presence of three haplotypes between polymorphic SNPs. read_haps is a tool that detects sample contamination from short read whole genome sequencing data. Availabilitygithub.com/DecodeGenetics/read_haps Contactbjarni.halldorsson@decode.is
- organism: human
- assay: whole-genome sequencing
- research focus: variant calling
- approach: experimental assay
- Citations
- 6
- FWCI
- 0.08
- Field percentile
- 36th percentile
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- hapCon: Estimating contamination of ancient genomes by copying from reference haplotypes
Yilei Huang, Harald Ringbauer·BioinformaticsPeer-reviewed·Jun 13, 2022
- HLA-MA: Simple yet powerful matching of samples using HLA typing results
Clemens Messerschmidt, Manuel Holtgrewe, Dieter Beule·BioinformaticsPeer-reviewed·Mar 9, 2017
- WhatsHap: fast and accurate read-based phasing
Marcel Martin, Murray Patterson, … Tobias Marschall·bioRxiv·Nov 14, 2016
- HuConTest: Testing human contamination in great ape samples
M. Kuhlwilm, C. Fontsere, … T. Marques-Bonet·bioRxiv·Mar 30, 2021
- devider: long-read reconstruction of many diverse haplotypes
Jim Shaw, Christina A. Boucher, … Heng Li·Lecture notes in computer sciencePeer-reviewed·Jan 1, 2025
- HapCHAT: Adaptive haplotype assembly for efficiently leveraging high coverage in long reads
Stefano Beretta, Murray Patterson, … Paola Bonizzoni·BMC BioinformaticsPeer-reviewed·Jul 3, 2018