Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

ABSTRACT:

Background

The analysis of next-generation sequencing data from large genomes is a timely research topic. Sequencers are producing billions of short sequence fragments from newly sequenced organisms. Computational methods for reconstructing whole genomes/transcriptomes (de novo assemblers) are typically employed to process such data. However, these methods require large memory resources and computation time. Many basic biological questions could be answered targeting specific information in the reads, thus avoiding complete assembly.

Results

We present Mapsembler, an iterative micro and targeted assembler which processes large datasets of reads on commodity hardware. Mapsembler checks for the presence of given regions of interest that can be constructed from reads and builds

SUBMITTER: Peterlongo P 

PROVIDER: S-EPMC3514201 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature