HASLR: Fast Hybrid Assembly of Long Reads

Haghshenas, Ehsan; Asghari, Hossein; Stoye, Jens; Chauve, Cédric; Hach, Faraz

doi:10.1016/j.isci.2020.101389

Cited by 53 publications

(49 citation statements)

References 44 publications

(86 reference statements)

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“…The short-read genomic data were also screened with these reference sequences using the bbduk tool in bbmap, and then normalized using bbnorm. With these refined read sets, we generated a final assembly using the hybrid assembler haslr (Haghshenas et al, 2020).…”

Section: Genome Assembly Decontamination and Genome Assessmentmentioning

confidence: 99%

A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

Weng

Francoeur

Currie

et al. 2021

Molecular Ecology Resources

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Beetles (Coleoptera) are the most diverse animal group on the planet, with more than 386,000 species described worldwide (Bouchard et al., 2017;Forbes et al., 2018). The extremely high diversity and abundance of beetles plays a critical role in most terrestrial ecosystems (Brooks et al., 2012;Erwin, 1997;Schowalter, 2013;Slade et al., 2019), with further significance to human society as they serve as food, pests, pets, biological control agents, and models in biological and engineering research (Adamski et al., 2019). Despite their importance, relatively few genomic studies have been conducted on beetles to date (McKenna, 2018).Coleoptera are divided into four suborders, Polyphaga, Adephaga, Myxophaga and Archostemata, based on both morphological and

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Section: Genome Assembly Decontamination and Genome Assessmentmentioning

confidence: 99%

A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

Weng

Francoeur

Currie

et al. 2021

Molecular Ecology Resources

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“…We compare results to the most widespread competing assembler Canu [ 10 ] and the faster Wtdbg2 [ 13 ], both demonstrating the disadvantages of long-read-only strategies especially in low coverage scenarios, although Wtdbg2 requires considerately less coverage in comparison. Additionally, we benchmarked two tools implementing the most closely related concept: DBG2OLC [ 23 ] and most recent competitor HASLR [ 21 ]. Finally, we added Wengan [ 19 ] as a leading but conceptually very unique alternative.…”

Section: Benchmarkingmentioning

confidence: 99%

“…HASLR [ 21 ] defines an assembly-graph-like structure, that includes both short and long reads. Short reads are assembled into contigs that, after k -mer filtering to remove repeats, are aligned to long reads.…”

Section: Introductionmentioning

confidence: 99%

LazyB: fast and cheap genome assembly

Gatter

Löhneysen

Fallmann

et al. 2021

Algorithms Mol Biol

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Background Advances in genome sequencing over the last years have lead to a fundamental paradigm shift in the field. With steadily decreasing sequencing costs, genome projects are no longer limited by the cost of raw sequencing data, but rather by computational problems associated with genome assembly. There is an urgent demand for more efficient and and more accurate methods is particular with regard to the highly complex and often very large genomes of animals and plants. Most recently, “hybrid” methods that integrate short and long read data have been devised to address this need. Results is such a hybrid genome assembler. It has been designed specificially with an emphasis on utilizing low-coverage short and long reads. starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs. This graph is translated into a long-read overlap graph G. Instead of the more conventional approach of removing tips, bubbles, and other local features, stepwisely extracts subgraphs whose global properties approach a disjoint union of paths. First, a consistently oriented subgraph is extracted, which in a second step is reduced to a directed acyclic graph. In the next step, properties of proper interval graphs are used to extract contigs as maximum weight paths. These path are translated into genomic sequences only in the final step. A prototype implementation of , entirely written in python, not only yields significantly more accurate assemblies of the yeast and fruit fly genomes compared to state-of-the-art pipelines but also requires much less computational effort. Conclusions is new low-cost genome assembler that copes well with large genomes and low coverage. It is based on a novel approach for reducing the overlap graph to a collection of paths, thus opening new avenues for future improvements. Availability The prototype is available at https://github.com/TGatter/LazyB.

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“…[14]. Hybrid (HY) assembly methods [15,16] using both SRs and LRs have been proposed to further reduce the error rates compared to LR-only assemblies. While Watson et al [14] showed that insertions/deletions (indels) play a critical role in microbial protein identification, the overall impact of assembly methods on understanding the functional potential of microbial communities is lacking.…”

Section: Introductionmentioning

confidence: 99%

Synergistic effect of short- and long-read sequencing on functional meta-omics

Galata¹,

Sb²,

Bj³

et al. 2021

Preprint

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Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-only, and hybrid assembly approaches on four different metagenomic samples of varying complexity and demonstrate how they affect gene and protein inference which is particularly relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic data-based protein predictions. Our findings pave the way for critical assessments of metagenomic reconstructions and we propose a reference-independent solution based on the synergistic effects of multi-omic data integration for the in situ study of microbiomes using long-read sequencing data.

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HASLR: Fast Hybrid Assembly of Long Reads

Cited by 53 publications

References 44 publications

A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

LazyB: fast and cheap genome assembly

Synergistic effect of short- and long-read sequencing on functional meta-omics

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