|Title||PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation.|
|Publication Type||Journal Article|
|Year of Publication||2021|
|Authors||Mahmoud, M, Doddapaneni, H, Timp, W, Sedlazeck, FJ|
|Date Published||2021 Sep 14|
|Keywords||Charcot-Marie-Tooth Disease, DNA Methylation, Genetic Variation, Genome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, Software|
Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.
|Alternate Journal||Genome Biol|
|PubMed Central ID||PMC8442460|
|Grant List||R01 HG009190 / HG / NHGRI NIH HHS / United States |
UM1 HG008898 / HG / NHGRI NIH HHS / United States
PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation.
|Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nat Commun. 2023;14(1):6113..|
|PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. Am J Hum Genet. 2023;110(10):1787-1803..|
|Chimeric RNAs reveal putative neoantigen peptides for developing tumor vaccines for breast cancer. Front Immunol. 2023;14:1188831..|