Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

Zerbino, Daniel R.; Birney, Ewan

doi:10.1101/gr.074492.107

Cited by 8,717 publications

(7,308 citation statements)

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“…We assembled the simulated reads into contigs with velvet v1.2.09 19 , then improved and annotated the resulting scaffolds 20 . We generated alignments by mapping reads to the TIGR4 reference using bwa-mem v0.7.10 with default settings 21 , and called variants from these alignments using samtools v1.2 mpileup and bcftools call 22 .…”

Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined “true tree” using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.

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Section: Methodsmentioning

confidence: 99%

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Lees¹,

Kendall²,

Parkhill³

et al. 2018

Wellcome Open Res

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“…DNA was sequenced on the Illumina GAII platform using 54‐bp paired‐end reads, resulting in a mean genome coverage of 1527 ×. A subset of Illumina reads was assembled using Velvet, version 1.0.12 (Zerbino & Birney, 2008), producing contiguous nucleotide sequences (contigs), which were scaffolded against the genome of strain F/SW4 (EMBL accession no. HE601804) (Harris et al ., 2012), using abacas (Assefa et al ., 2009).…”

Section: Methodsmentioning

confidence: 99%

Plasmid deficiency in urogenital isolates ofChlamydia trachomatisreduces infectivity and virulence in a mouse model

et al. 2013

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We hypothesized that the plasmid of urogenital isolates of Chlamydia trachomatis would modulate infectivity and virulence in a mouse model. To test this hypothesis, we infected female mice in the respiratory or urogenital tract with graded doses of a human urogenital isolate of C. trachomatis, serovar F, possessing the cognate plasmid. For comparison, we inoculated mice with a plasmid‐free serovar F isolate. Following urogenital inoculation, the plasmid‐free isolate displayed significantly reduced infectivity compared with the wild‐type strain with the latter yielding a 17‐fold lower infectious dose to yield 50% infection. When inoculated via the respiratory tract, the plasmid‐free isolate exhibited reduced infectivity and virulence (as measured by weight change) when compared to the wild‐type isolate. Further, differences in infectivity, but not in virulence were observed in a C. trachomatis, serovar E isolate with a deletion within the plasmid coding sequence 1 when compared to a serovar E isolate with no mutations in the plasmid. We conclude that plasmid loss reduces virulence and infectivity in this mouse model. These findings further support a role for the chlamydial plasmid in infectivity and virulence in vivo.

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“…The Rnnotator 16 , Multiple-k 21 , and Trans-ABySS 19 assemblers follow the same strategy; they assemble the dataset multiple times using a De Bruijn graph-based approach [6][7][8]58 to reconstruct transcripts from a broad range of expression levels, and then post-process the assembly to merge contigs and remove redundancy (Figure 2b). By contrast, other assemblers (Trinity 59 , and Oases 20 ) traverse the De Bruijn graph directly to assemble each isoform.…”

Section: De Novo Strategymentioning

confidence: 99%