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

By Marten Boetzer, Walter Pirovano. BMC Bioinformatics, 2014

479 citations recorded by the source corpus.

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. 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. 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.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2399ca37840b4d6569d7f5de4f1a5ff499c89311

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

1. Hengyun Lu
2. Zemin Ning
3. Francesca Giordano
4. W. D. de Vos
5. Jerzy K. Kulski
6. Computational Pan-Genomics Consortium

In Genetics

1. David J. Studholme
2. Hengyun Lu
3. Zemin Ning
4. Francesca Giordano
5. W. D. de Vos

In Molecular Biology

1. H. Smidt
2. David J. Studholme
3. Hengyun Lu
4. J. Gerritsen
5. Zemin Ning
6. Ger T. Rijkers
7. Francesca Giordano
8. W. D. de Vos

Citations in the corpus

• TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads (2020, unknown): “Most construct a final assembly graph by mixing NGS contigs and TGS long reads based on the Overlap-Layout-Consensus or string graph algorithm [21], or connect the contigs generated by NGS with their alignments against long reads [22–24].”
• A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle (2019, methodology): “Scaffolding of the contigs was done with SSPACE-LongRead (30) and the PacBio CCS reads using default settings.”
• Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “LongRead [32] and SMIS [33] are also included in the table as they are not complete pipelines for de novo assemblies.”
• Assessing the performance of the Oxford Nanopore Technologies MinION (2015, methodology): “ssembled from short reads [3,31] and resolving repeat sequences r haplotypes, being able to span ambiguous regions in a single ead, as has been demonstrated for PacBio [27,9].”