Meta-IDBA statistics

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Meta-IDBA specifications


Unique identifier OMICS_01425
Name Meta-IDBA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No


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Publication for Meta-IDBA

Meta-IDBA in publications

PMCID: 5698827
PMID: 29250541
DOI: 10.1155/2017/4740354

[…] sequencing reads come from thousands of highly uneven different species, and it cannot provide a high sequencing coverage of single species. several de novo metagenomic short read assemblers such as meta-idba [], idba-ud [], ray meta [], metavelvet-sl [], omega [], and metaspades [] have shown promising results and effectiveness in assembling metagenomic short reads, but they do not work well […]

PMCID: 5668418
PMID: 29097759
DOI: 10.1038/s41598-017-14576-6

[…] and 200 and applied the same optimisation criteria as for the metavelvet assemblies resulting in an overlap length of 140 for e. prunastri and 150 for p. furfuracea. idba-ud was chosen instead of meta-idba as it generally performs better according to the authors and was run with k-mer sizes from 51 to 231 with a step size of 20. all resulting assemblies of all assemblers were filtered […]

PMCID: 5242441
PMID: 28099457
DOI: 10.1371/journal.pone.0169662

[…] version accepts k-mer lengths up to 128., idba (iterative de bruijn graph de novo assembler) is a suite of different de bruijn graph based assemblers, each dedicated for a specific task. originally, meta-idba was developed for metagenome assembly []. this tool attempts to conserve and reconstruct micro variations between closely related sub-strains by partitioning the assembly graph […]

PMCID: 5346311
PMID: 27697111
DOI: 10.5483/BMBRep.2016.49.12.164

[…] successfully used to assemble contigs using an optimized soapdenovo protocol (). recently, more sophisticated algorithms have been developed and applied to the next-generation assemblers, such as meta-idba (), metavelvet-sl () and idba-ud ()., following reconstruction, next stage is to identify genes in the reads or assembled contigs and/or scaffolds. the prediction of genes in metagenomic […]

PMCID: 5137872
PMID: 27918579
DOI: 10.1371/journal.pcbi.1005224

[…] that contains the topology of the de bruijn graph in addition to the contig sequences (each corresponding to an edge in the graph). many other metagenome assembly algorithms (e.g., metavelvet [] and meta-idba []) are based on the data structure of de bruijn graph, which, however do not output the graph structure explicitly. as a successor of soapdenovo for metagenome assembly, the megahit […]

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Meta-IDBA institution(s)
Department of Computer Science, The University of Hong Kong, Hong Kong

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