PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

ABSTRACT:

Motivation

The explosion of next-generation sequencing data has spawned the design of new algorithms and software tools to provide efficient mapping for different read lengths and sequencing technologies. In particular, ABI's sequencer (SOLiD system) poses a big computational challenge with its capacity to produce very large amounts of data, and its unique strategy of encoding sequence data into color signals.

Results

We present the mapping software, named PerM (Periodic Seed Mapping) that uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared with state-of-the-art programs. The data structure in PerM requires only 4.5 bytes per base to index the human genome, allowing entire genomes to be loaded to memory, while mult

SUBMITTER: Chen Y 

PROVIDER: S-EPMC2752623 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature