Search Results for "hash table"

TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference. TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. We have shown that TAG helps to assemble substantially more transcripts from metatranscriptomic datasets that otherwise would have been missed or truncated because of the fragmented nature of the reference metagenome. ...

This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment.

A general purpose distributed hash table adapted for sequence analysis. This program searches for all maximal, exact unique n-mers from a given set of genomes. Originally, this program's primary use was to design resequencing microarrays.