Axe: rapid, competitive sequence read demultiplexing using a trie

An Efficient Trie Hashing Method Using a Compact Binary Trie

In many applications, information retrieval is a very important research eld. In several key strategies, the binary trie is famous as a fast access method to be able to retrieve keys in order. However, if the binary trie structure is implemented, the greater the number of the registered keys, the larger storage is required, as a result, the binary trie can not be stored into the main memory. In...

Trie-Based Data Structures for Sequence Assembly

We investigate the application of trie-based data structures, suux trees and suux arrays in the problem of overlap detection in fragment assembly. Both data structures are theoretically and experimentally analyzed on speed and space. By using heuristics, we can greatly reduce the calls to the time-consuming dynamic programming, and have improved the speed of overlap detection up to 1,000 times ...

The Sequence Read Archive

The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequen...

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

Motivation The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functiona...

Trie - Based Data Structures for Sequence Assembly ( Extended Abstract ) Ting