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IDBA specifications

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Unique identifier OMICS_20110
Name IDBA
Alternative name Iterative De Bruijn graph de novo Assembler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.1.1
Stability Stable
Maintained No

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Publication for Iterative De Bruijn graph de novo Assembler

IDBA in publications

 (7)
PMCID: 5776456
PMID: 29099492
DOI: 10.1038/ismej.2017.175

[…] than 20, were discarded. nonpareil () was used to estimate the coverage of the community on each metagenome data set with default parameters. de novo assemblies of trimmed reads were generated using idba assembler () with the ‘-pre_correction’ option resulting in two large contigs (over 20 kb) that were then merged as described in . functional annotation of predicted genes from virus metagenomes […]

PMCID: 5497025
PMID: 28685163
DOI: 10.1128/mSphereDirect.00257-17

[…] illumina sequences from each sample were first trimmed from both the 5′ and 3′ ends with sickle (https://github.com/najoshi/sickle), and then each sample was assembled individually with idba-ud (iterative de bruijn graph de novo assembler for short-read sequencing data with highly uneven sequencing depth) (, ) by using default parameters. unassembled illumina reads from input and produced […]

PMCID: 5563965
PMID: 28524866
DOI: 10.1038/ismej.2017.78

[…] to generate longer contigs and allow for the highest likelihood of producing near-complete genomic bins, the reads from all eight metagenomes were concatenated, normalized, then assembled using an iterative de bruijn graph de novo assembler for uneven sequencing depth data (idba-ud) () as detailed in . resulting bins were analyzed for quality and completeness against single copy genes using […]

PMCID: 4563136
PMID: 26425705
DOI: 10.1016/j.ebiom.2015.07.007

[…] on average, 76.0 million ± 18.0 million (mean ± s.d.) reads for each sample were retained and used for further analysis., high-quality reads were used for de novo assembly with idba-ud () (an iterative de bruijn graph de novo assembler) into contigs of at least 500 bp. reads from all samples from the same volunteer were assembled. genes were predicted using metagenemark (). […]

PMCID: 4486115
PMID: 26044993
DOI: 10.1007/s00284-015-0846-2

[…] sliding window approach to trim regions when the average base quality dropped below 20. a 10-bp length threshold was used to discard reads that fall below this length after trimming. idba-ud [], an iterative de bruijn graph de novo assembler, was used to assemble contigs by iterating from kmer size of 21–121 and using a pre-correction of reads before assembly. we obtained assembled contigs […]


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

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