Download our soft from

(alternative download url:


Motivation: It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the Second Generation Sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the Single-Molecule Real-Time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost, and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity, and variability of coverage. However, current assemblers of SGS data do not sufficiently take advantage of the OLC approach.

Results: Aiming at minimizing uncertainty, the proposed method BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. The tests on two eukaryote genomes, a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus, show that BAUM achieved substantial improvement on genome size and continuity. Besides, BAUM reconstructed a considerable amount of repetitive regions that failed to be assembled by existing short read assemblers. We also propose statistical approaches to control the uncertainty in different steps of BAUM.


Categories: BioinformaticsSoft

Leave a Reply

Your email address will not be published. Required fields are marked *

Related Posts



PHRAP 2007 Assembling Genomic DNA Sequences with PHRAP Cold Spring Harbor Laboratory Current protocols in bioinformatics   Related


SGS genome assembly Platform

2010 Sequencing technologies — the next generation Human Genome Sequencing Center and Department of Molecular & Human Genetics, Baylor College of Medicine Nature reviews Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and Read more…


Long reads genome assembly 2015 Assembling large genomes with single-molecule sequencing and locality-sensitive hashing Department of Chemistry and Biochemistry, University of Maryland Nature Biotechnology   Related

%d bloggers like this: