Results for "segmental"
Blogs
Structural variation: the hidden genomic treasure
...ted fork stalling and template switching. CNVs are closely related to segmental duplications (SDs): SDs can s...k stalling and template switching (FoSTeS). CNV is closely linked to segmental duplication, but is not exact...2712 days ago
Bookmarks
mrFAST: Micro Read Fast Alignment Search Tool
...ST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps sho...2940 days ago
DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
...conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be re...2643 days ago
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Top-level pages
List of Bioinformatics Software Tools for Next Generation Sequencing
...on annotation, selected ENCODE annotation, allele frequency in the 1000 Genomes Project, allele frequency in the Exome Variant Server (ESP6500), segmental duplication annotation, SIFT,...2918 days ago
Tools for Searching Repeats And Palindromic Sequences
...c.Tandem Repeats - Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base sequences.Segmental Duplications - Large blocks o...2220 days ago
Tags
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs. ht...Tags: SDA, Long-read, sequence, assembly, segmental, duplications
1897 days ago
- HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. More at https://www.biorxiv.org/content/10.1101/2020.03.14.992248v3
Tags: HiCanu, accurate, assembly, segmental, duplications, satellites, allelic, variants, high-fidelity, long, reads
1508 days ago
Comments
Comment on "Genome in a Bottle (GIAB) Consortium"
...riant calls, as well as calls in difficult genomic contexts (e.g., homopolymers/tandem repeats and difficult-to-map regions like pseudogenes and segmental duplications). GIAB is...1569 days ago
Comment on "Structural variation: the hidden genomic treasure"
...h Hydra. However, it should be noted that this approach seeks to discover breakpoints arising from both "unique" and duplicated (e.g., segmental duplications, recent retrotra...2711 days ago
