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MARS: a tool for haplotype-resolved population-based structural variation detection Open
Motivation Linked-reads enables genome-wide phased diploid assemblies. These haplotype-resolved assemblies allow us to genotype structural variants (SVs) with a high sensitivity and be able to further phase them. Yet, existing SV callers a…
De novo mutational signature discovery in tumor genomes using SparseSignatures Open
Cancer is the result of mutagenic processes that can be inferred from tumor genomes by analyzing rate spectra of point mutations, or “mutational signatures”. Here we present SparseSignatures, a novel framework to extract signatures from so…
Example dataset of stLFR linked reads to run Aquila_stLFR Open
We provide this small chromosome (chr21) example dataset to run Aquila_stLFR. Aquila_stLFR: https://github.com/maiziex/Aquila_stLFR
Example dataset of stLFR linked reads to run Aquila_stLFR Open
We provide this small chromosome (chr21) example dataset to run Aquila_stLFR. Aquila_stLFR: https://github.com/maiziex/Aquila_stLFR
Example dataset of stLFR linked reads to run Aquila_stLFR Open
We provide this small chromosome (chr21) example dataset to run Aquila_stLFR. Aquila_stLFR: https://github.com/maiziex/Aquila_stLFR
Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads Open
Motivation Identifying structural variants (SVs) is critical in health and disease, however, detecting them remains a challenge. Several linked-read sequencing technologies, including 10X Genomics, TELL-Seq and single tube long fragment re…
Benchmarking challenging small variants with linked and long reads Open
Summary Genome in a Bottle (GIAB) benchmarks have been widely used to help validate clinical sequencing pipelines and develop new variant calling and sequencing methods. Here, we use accurate linked reads and long reads to expand the prior…
De novo diploid genome assembly for genome-wide structural variant detection Open
Detection of structural variants (SVs) on the basis of read alignment to a reference genome remains a difficult problem. De novo assembly, traditionally used to generate reference genomes, offers an alternative for SV detection. However, i…
Assessment of human diploid genome assembly with 10x Linked-Reads data Open
Background Producing cost-effective haplotype-resolved personal genomes remains challenging. 10x Linked-Read sequencing, with its high base quality and long-range information, has been demonstrated to facilitate de novo assembly of human g…
Assessment of human diploid genome assembly with 10x Linked-Reads data Open
Background Producing cost-effective haplotype-resolved personal genomes remains challenging. 10x Linked-Read sequencing, with its high base quality and long-range information, has been demonstrated to facilitate de novo assembly of human g…
Aquila: diploid personal genome assembly and comprehensive variant detection based on linked reads Open
Variant discovery in personal, whole genome sequence data is critical for uncovering the genetic contributions to health and disease. We introduce a new approach, Aquila, that uses linked-read data for generating a high quality diploid gen…
<i>De novo</i> diploid genome assembly for genome-wide structural variant detection Open
Structural variants (SVs) in a personal genome are important but, for all practical purposes, impossible to detect comprehensively by standard short-fragment sequencing. De novo assembly, traditionally used to generate reference genomes, o…
Additional file 9: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S4. Exposure values (number of mutations attributed to each signature) for each of the 9 signatures, in each of the 555 breast tumors in which signatures were discovered. (XLSX 133 kb)
Additional file 13: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S8. Validation of interchromosomal translocations in BRCA1-mutated tumors using 10X genomics. (XLSX 9 kb)
Additional file 6: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S1. 9 signatures (including the background) discovered by SparseSignatures on the whole genomes of 560 breast tumors. (XLSX 20 kb)
Additional file 14: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S9. Comparison of the 9 signatures (including background) obtained by SparseSignatures with those obtained in a previous study [11]. (XLSX 9 kb)
Additional file 12: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S7. Details of 10-Mb genomic bins with significant enrichment of structural variant breakpoints, in the combined genomes of 46 BRCA1/2 mutated tumors. (XLSX 44 kb)
Additional file 15: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S10. Exposure values (number of mutations attributed to each signature) for each of the 10 signatures discovered by applying SparseSignatures to a pan-cancer dataset of 2827 tumors [21], in each of 560 breast tumors, in the genomes o…
Additional file 7: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S2. Cosine similarities between the 9 signatures (including the background) discovered by SparseSignatures on the whole genomes of 560 breast tumors, and the 30 signatures in the COSMIC database ( https://cancer.sanger.ac.uk/cosmic/s…
Additional file 8: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S3. Cosine similarities between the 9 signatures (including the background) discovered by SparseSignatures on the whole genomes of 560 breast tumors. (XLSX 36 kb)
Additional file 11: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S6. Details of the 81 samples used for structural variant analysis with SvABA. (XLSX 11 kb)
Additional file 10: of Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations Open
Table S5. Details of the 771 samples from TCGA used for DNA methylation analysis. (XLSX 85 kb)
Comprehensive Genomic Characterization of Breast Tumors with BRCA1 and BRCA2 Mutations Open
Background Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients. Here we present a …
De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures Open
Cancer is the result of mutagenic processes that can be inferred from tumor genomes by analyzing rate spectra of point mutations, or “mutational signatures”. Here we present SparseSignatures, a novel framework to extract signatures from so…
View article: genomeview - an extensible python-based genomics visualization engine
genomeview - an extensible python-based genomics visualization engine Open
Visual inspection and analysis is integral to quality control, hypothesis generation, methods development and validation of genomic data. The richness and complexity of genomic data necessitates customized visualizations highlighting speci…