De novo assembly of highly repetitive genomes using noisy long-readsMartin Pippel
Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces...
In genome assembly, the primary issue is how to determine upstream and downstream sequence regions of sequence seeds for constructing long contigs or scaffolds. When extending one sequence seed, repetitive regions in the genome always cause multiple feasible extension candidates which increase the difficu...
De novo assembly of large, highly repetitive and highly heterozygous eukaryotic genomes from short-read data remains a challenge. In transcriptome studies, 454 pyrosequencing has proven very useful for generating ESTs representing the majority of expressed genes. This has enabled gene discovery in a ...
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits 来自 掌桥科研 喜欢 0 阅读量: 747 摘要: Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the ...
Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes Ko Ikemoto , Hinano Fujimoto & Akihiro Fujimoto Human Genomics Open Access 09 March 2023 Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics ...
Additional file 1:Venn diagram of the number of genes annotated as non-functional, i.e. containing frame-shift mutations or PTCs, in thede novotranscriptome assembly and the genome assembly of[9]. This diagram is based on a total of 1,460 neo-Y genes that were allocated to the Muller ...
repetitive genomic regions. To this end, they have become the mainstream method of sequencing for genome assembly. The high-fidelity (HiFi) reads recently produced by PacBio display superior performance to de novo assembly [3,4,5]. However, they generally have an average length of ~ 15 ...
Figure 2. Process of de novo assembly of the complete plant genomes. Sequencing platform, software, precautions, etc are noted in the figure alongside the steps. DownLoad: Full-Size Img PowerPoint Tools for genome assembly of ultra-long reads The huge amounts of data of the second-generat...
Etienne Bucher and colleagues use a combination of short- and long-read sequencing, along with optical mapping technologies, to produce the high-quality de novo assembly of the apple genome. They identify a new repetitive retrotransposon sequence and ana