Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an ...
2017. Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases. Genome Med 9: 57. http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-017-0447-8.Greer,S.U., Nadauld,L.D., Lau,B.T., Chen,J., Wood-Bouwens,C., Ford,J.M., Kuo,C.J. and ...
A haplotype switching molecule may be generated from a true recombinant molecule or alternatively represent a false positive caused by bioinformatic errors, such as sequencing error, incorrect read mapping, structural variation, or barcode sharing among molecules from the same part of the genome. Our ...
Linker - Tools for Analyzing Long and Linked Read Sequencing Table of Contents Installation Description Commands Input/Output Installation This code requires bamtools, htslib, c++11, and zlib libraries. htslib: https://github.com/samtools/htslib bamtools: https://github.com/pezmaster31/bamtools From...
ARCS and ARKS are genome sequence assembly scaffolders using linked and long read sequencing data Run modes - cheat sheet ARCS can be run in 4 modes: ARCS(default) uses alignments of linked reads to the input contigs ARCS-long (arcs-long) uses alignments of long reads to the input contigs...
Linked-read sequencing provides long-range information on short-read sequencing data by barcoding reads originating from the same DNA molecule, and can improve detection and breakpoint identification for structural variants (SVs). Here we present LinkedSV for SV detection on linked-read sequencing data...
We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes usi... - 《Nature Biotechnology》 被引量: 205发表: 2016年 A hybrid approach for de novo human genome sequence assembly and phasing The combination of short-read sequence ...
We present Samovar, a mosaic single-nucleotide variant (SNV) caller for linked-read whole-genome shotgun sequencing data. Samovar scores candidate sites using a random forest model trained using the input dataset that considers read quality, phasing, and linked-read characteristics. We show Samovar...
to detect de novo mutations on barcoded linked read sequencing. We identified the major source of de novo mutation from NGS data was caused by the biased haplotype coverage. HAPDeNovo can eliminate more than 99% false positive de novo calls with the help of 10X linked read sequencing. ...
To investigate the characteristics of genes that are susceptible to alternative splicing, we performed linear regression with the objective variable as the number of alternatively spliced isoforms and the explanatory variable as the read counts of genes in long-read sequencing. Then, we extracted genes...