Format

Send to

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2014 Jun 20;15:211. doi: 10.1186/1471-2105-15-211.

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

Author information

1
BaseClear B,V,, Genome analysis and technology department, Einsteinweg 5, Leiden 2333 CC, The Netherlands. walter.pirovano@baseclear.com.

Abstract

BACKGROUND:

The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data.

RESULTS:

Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes.

CONCLUSIONS:

The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner.

PMID:
24950923
PMCID:
PMC4076250
DOI:
10.1186/1471-2105-15-211
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Support Center