RESUMO
Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.
Assuntos
Genoma Humano , Genômica , Masculino , Humanos , Complexo Principal de HistocompatibilidadeRESUMO
UNLABELLED: We introduce FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance. AVAILABILITY AND IMPLEMENTATION: The tool and data are available and will be maintained at http://kakitone.github.io/finishingTool/ CONTACT: : dntse@stanford.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Assuntos
Algoritmos , Biologia Computacional/métodos , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequências Repetitivas de Ácido Nucleico/genética , Análise de Sequência de DNA/métodos , Software , Animais , Caenorhabditis elegans/genética , Drosophila/genética , Modelos Estatísticos , Saccharomyces cerevisiae/genéticaRESUMO
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption of no errors in the reads (noiseless reads). In this work, we show that even when there is noise in the reads, one can successfully reconstruct with information requirements close to the noiseless fundamental limit. A new assembly algorithm, X-phased Multibridging, is designed based on a probabilistic model of the genome. It is shown through analysis to perform well on the model, and through simulations to perform well on real genomes.