Journal: Bioinformatics

Article Title: Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

doi: 10.1093/bioinformatics/btu436

Figure Lengend Snippet: Comparison of RC normalization and accuracy of CNV calls achieved by ONCOCNV, ADTEx and NextGENe for samples from dataset A. ( A ) Correlation between NRCs and log ratio values of array CGH. ( B ) Prediction accuracy. Accuracy = (#True predictions)/(#All predictions), where each prediction corresponds to a gene copy number status (gain, neutral or loss). ( C ) True-positive rate. ( D ) False-positive rate

Article Snippet: We decided to compare our CNA calling method in ultra-deep targeted sequencing data with two WES-specific tools: ADTEx ( Amarasinghe et al. , 2013 ), a method based on hidden Markov models (HMMs) for CNA calling in targeted (exome) sequencing data, and NextGENe, commercial software designed by SoftGenetics.

Techniques: Comparison

Journal: Bioinformatics

Article Title: Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

doi: 10.1093/bioinformatics/btu436

Figure Lengend Snippet: Example of CNVs called by ONCOCNV, ADTEx and NextGENe (Sample A1). ( A) Array CGH profile for sample A1, segmented using cghseg: purple (loss), orange (gain). x -axis corresponds to probe indexes. ( B) Copy number profile calculated by ONCOCNV. x -axis corresponds to amplicon indexes. ( C) Agreement between CNVs predicted from array CGHs and amplicon sequencing. Each vertical bar denotes a gene copy number status: white (neutral), purple (loss) and orange (gain)

Article Snippet: We decided to compare our CNA calling method in ultra-deep targeted sequencing data with two WES-specific tools: ADTEx ( Amarasinghe et al. , 2013 ), a method based on hidden Markov models (HMMs) for CNA calling in targeted (exome) sequencing data, and NextGENe, commercial software designed by SoftGenetics.

Techniques: Amplification, Sequencing

Journal: Nature Communications

Article Title: Targeted sequencing and iterative assembly of near-complete genomes

doi: 10.1038/s41467-025-65410-x

Figure Lengend Snippet: a Overview of the Cornetto method. A primary assembly generated from whole-genome LRS data (PacBio HiFi or ONT), provides the starting reference. Regions with poor coverage, mappability, assembly quality, short contigs and contig ends are identified. The remainder are considered ‘boring bits’ and labelled for rejection by ONT ReadUntil. Sequencing is paused at regular intervals (e.g. 24, 48, 72 h) and new assembly is generated, providing an updated reference and boring bits. Sequencing is resumed after washing and re-loading flow cell. Data is focused onto an increasingly small and challenging portion of the genome. b For a given primary assembly, Nx plots show contigs sizes sorted from largest to smallest, relative to cumulative assembly size, as a percentage of human genome (3.1 Gbase). Each line shows n = 1 assembly. Assemblies were generated using LRS data from hg002. T2T-chm13 is shown for comparison (grey line). Sub-panels show: (i) Assemblies of HiFi data from 1, 2 or 3 SMRT cells. (ii) Combined data from 1 SMRT cell and 3 ONT duplex flow cells ( hg002-NonCornetto-1 ); or 1 SMRT cell and 9 duplex flow cells ( hg002-NonCornetto-2 ). (iii, iv) Two Cornetto experiments ( hg002-Cornetto-1 / -2 ), each using 1 SMRT Cell and 3 duplex flow cells run sequentially with 3 cycles per cell, resulting in 9 intermediate assemblies. c For the same assemblies, tile plot shows contiguity of human chromosomes. Colour scale encodes L 90 values: number of contigs encompassing >90% of the reference sequence for a given chromosome. Dark purple tiles show chromosomes with L 90 = 1 and a telomere detected at each end, indicating the whole chromosome is assembled as a single primary contig.

Article Snippet: Current best practices call for a combination of deep Pacific Biosciences (PacBio) HiFi LRS data, coupled with Oxford Nanopore Technologies (ONT) ultra-long LRS data and Illumina Hi-C chromatin conformation capture, or an analogous long-range sequencing method .

Techniques: Generated, Sequencing, Comparison

Journal: Nature Communications

Article Title: Targeted sequencing and iterative assembly of near-complete genomes

doi: 10.1038/s41467-025-65410-x

Figure Lengend Snippet: a Nx plot shows contig sizes sorted from largest to smallest, relative to cumulative assembly size, as a percentage of the haploid genome size for each species. From left to right the plots show genome assemblies for: Gould’s petrel ( Pterodroma leucoptera ); redstriped eartheater cichlid ( Geophagus surinamensis ); orange-bellied parrot ( Neophema chrysogaster ); western saw-shelled turtle ( Myuchelys bellii ; see Supplementary Note ). The petrel and cichlid were assembled with PacBio HiFi (1 SMRT cell; base) plus ONT duplex data (2 duplex cells; cornetto). The parrot and turtle were assembled using ONT data, one or two standard flow cells (base) plus another with adaptive sequencing (Cornetto; simplex reads; LSK114). For ONT-only experiments, diploid assemblies were generated and haplotypes are plotted separately. b For the petrel and turtle assemblies above, bar plots show sizes of the fifty largest contigs in descending order, coloured according to presence of telomere sequences at contigs ends (both ends = purple; one end = pink). Equivalent plots for the cichlid and parrot are shown in Supplementary Fig. . c Bar plots show standard quality metrics for the same assemblies as in ( a ). From left to right, these are: contig N 50 lengths in Mbases; number of complete chromosomes (>1 Mbase and telomere detected at both ends); proportion of BUSCO genes detected as complete, duplicated, fragmented or missing. All plots show data for n = 1 assembly.

Article Snippet: Current best practices call for a combination of deep Pacific Biosciences (PacBio) HiFi LRS data, coupled with Oxford Nanopore Technologies (ONT) ultra-long LRS data and Illumina Hi-C chromatin conformation capture, or an analogous long-range sequencing method .

Techniques: Western Blot, Sequencing, Generated