Journal: bioRxiv

Article Title: Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite Plasmodium yoelii 17XNL

doi: 10.1101/2023.01.06.523040

Figure Lengend Snippet: (Left) Genome Assembly: High-accuracy ccs reads that were generated from PacBio subreads and trimmed Nanopore reads were de novo assembled to create draft genomes. Contigs were selected, and chromosome names were assigned based on the P. yoelii 17X reference genome alignment. Further processing of the Nanopore + Illumina hybrid assembly involved implementing scaffolding and iterative polishing. (Right) Gene-model prediction: A Nanopore dRNA-seq-based gene model and a hybrid gene model combining both Nanopore dRNA-seq and Illumina RNA-seq data were generated using Braker2. The predicted genes were annotated using reciprocal BLAST against P. yoelii 17X proteins. Illumina RNA-seq reads were previously reported .

Article Snippet: Even without any polishing efforts, this approach outperformed a parallel effort using a hybrid Nanopore long-read DNA-seq/Illumina short-read DNA-seq method by several key metrics, including its assembly quality and the reduction of gaps.

Techniques: Generated, Scaffolding, RNA Sequencing

Journal: Therapeutic Advances in Medical Oncology

Article Title: The diagnostic accuracy of PIK3CA mutations by circulating tumor DNA in breast cancer: an individual patient data meta-analysis

doi: 10.1177/17588359221110162

Figure Lengend Snippet: Comparison of tissue versus ctDNA for detection of PIK3CA mutations according to technique and performance.

Article Snippet: , Plasma , Hybrid capture-based NGS (Hi-Seq, Illumina) (FoundationACT ctDNA assay) , E542K; E545K; H1047R; H1047L , E545K (1); H1047L (1); H1047R (1); E726K (1) , ctDNA− , 0 , 11 , 11 , Specificity , 100.

Techniques: Comparison, Mutagenesis, Diagnostic Assay, Clinical Proteomics, Sequencing, Digital PCR, Amplification, Hybridization