[PDF][PDF] Computational pan-genomics: status, promises and challenges
Briefings in bioinformatics, 2018 - academic.oup.com
Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …
A survey of sequence alignment algorithms for next-generation sequencing
Rapidly evolving sequencing technologies produce data on an unparalleled scale. A central
challenge to the analysis of this data is sequence alignment, whereby sequence reads must …
challenge to the analysis of this data is sequence alignment, whereby sequence reads must …
Fully functional suffix trees and optimal text searching in BWT-runs bounded space
Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …
versioned text collections—has become an important problem since the turn of the …
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
H Li - Bioinformatics, 2012 - academic.oup.com
Abstract Motivation: Eugene Myers in his string graph paper suggested that in a string graph
or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also …
or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also …
[图书][B] Genome-scale algorithm design
High-throughput sequencing has revolutionised the field of biological sequence analysis. Its
application has enabled researchers to address important biological questions, often for the …
application has enabled researchers to address important biological questions, often for the …
Optimal-time text indexing in BWT-runs bounded space
Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …
versioned text collections—has become an important problem since the turn of the …
Relative Lempel-Ziv compression of genomes for large-scale storage and retrieval
S Kuruppu, SJ Puglisi, J Zobel - International Symposium on String …, 2010 - Springer
Self-indexes–data structures that simultaneously provide fast search of and access to
compressed text–are promising for genomic data but in their usual form are not able to …
compressed text–are promising for genomic data but in their usual form are not able to …
Alignment of next-generation sequencing reads
High-throughput DNA sequencing has considerably changed the possibilities for conducting
biomedical research by measuring billions of short DNA or RNA fragments. A central …
biomedical research by measuring billions of short DNA or RNA fragments. A central …
Short read alignment with populations of genomes
The increasing availability of high-throughput sequencing technologies has led to
thousands of human genomes having been sequenced in the past years. Efforts such as the …
thousands of human genomes having been sequenced in the past years. Efforts such as the …
Optimized succinct data structures for massive data
Succinct data structures provide the same functionality as their corresponding traditional
data structure in compact space. We improve on functions rank and select, which are the …
data structure in compact space. We improve on functions rank and select, which are the …