2010
DOI: 10.1007/978-3-642-12683-3_28
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IDBA – A Practical Iterative de Bruijn Graph De Novo Assembler

Abstract: Abstract. The de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs. The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides. Both approaches must deal with the following problems: false-positive vertices, due to erroneous reads; gap problem, due to non-uniform coverage; branching problem, due to erroneous reads and repeat regions. A proper choice of k is crucial but for single k there is always a trade-off: a small k favor… Show more

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Cited by 237 publications
(197 citation statements)
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“…As a result, the speed of IDBA-UD is similar to the performance of existing algorithms [13]. Moreover, we can jump from k to k+s instead of considering every k between k min and k max to speed up the assembling process.…”
Section: Multiple Kmentioning
confidence: 70%
See 3 more Smart Citations
“…As a result, the speed of IDBA-UD is similar to the performance of existing algorithms [13]. Moreover, we can jump from k to k+s instead of considering every k between k min and k max to speed up the assembling process.…”
Section: Multiple Kmentioning
confidence: 70%
“…The de Bruijn graph approach, e.g., Velvet [11], Abyss [12], IDBA [13][14][15][16][17][18], Euler-SR [19,20] and AllPaths [21], constructs a de Bruijn graph for the reads in which each vertex represents a length-k substring (k-mer) in a read and there is a directed edge from vertex u to vertex v if u and v are consecutive k-mers in a read, i.e., the last k-1 nucleotides of the k-mer represented by u is the same as the first k-1 nucleotides of the k-mer represented by v. Similar to the string graph approach, maximal paths without branches in the graph corresponding to contigs are outputted. There are two main advantages against the other two approaches.…”
Section: Existing Approachesmentioning
confidence: 99%
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“…We compared Pathset to Velvet (Zerbino and Birney, 2008), SOAPdenovo (Li et al, 2010), SPAdes (Bankevich et al, 2012), and IDBA (Peng et al, 2010) assemblers using Plantagora (Young et al, 2011), an assembly evaluation tool (see Table 2) For dataset EC215, Pathset improved on other assemblers in N50, N75, number of misassemblies, 8 and the number of captured complete genes. For dataset EC500, Pathset outperformed the other assemblers in N75 and the number of captured genes.…”
Section: Comparing Pathset With Other Genome Assemblersmentioning
confidence: 99%