Meta-IDBA statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Assembly chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Meta-IDBA specifications

Information


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

Versioning


Add your version

Maintainer


This tool is not maintained anymore.

Publication for Meta-IDBA

Meta-IDBA in publications

 (16)
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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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

Meta-IDBA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Meta-IDBA