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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 citations

 (13)
library_books

Characterization of ecologically diverse viruses infecting co occurring strains of cosmopolitan hyperhalophilic Bacteroidetes

2017
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 […]

library_books

An NGS based approach for the identification of sex specific markers in snakehead (Channa argus)

2017
Oncotarget
PMCID: 5716763
PMID: 29228723
DOI: 10.18632/oncotarget.21924

[…] r females. This might relate to the generation of the male-specific contigs, which was mentioned in Acquisition of the candidate Y chromosome-specific fragments. There were some splicing errors using IDBA to assemble these 60 bp short fragments, and primers based on these “coined” contigs would fail to amplify any products. In support of this, subsequent analysis uncovered that about 125 splicing […]

library_books

Succession in the petroleum reservoir microbiome through an oil field production lifecycle

2017
PMCID: 5563965
PMID: 28524866
DOI: 10.1038/ismej.2017.78

[…] 1. 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 Che […]

library_books

Draft Genome Sequences of the Aerobic Strains Lactobacillus gasseri AL3 and AL5

2017
Genome Announc
PMCID: 5442371
PMID: 28473372
DOI: 10.1128/genomeA.00213-17

[…] (AL3) and 12,136,300 (AL5) paired-end reads. Low-quality bases (Phred score <20) were trimmed, and reads shorter than 60 bp were discarded using the SolexaQA++ software (). Reads were assembled using IDBA version 1.1.1 (), and assembly was improved by using SSPACE (). Genes were predicted with PROKKA (). Predicted genes were queried in the NCBI database against proteins involved in aerobic (pyruva […]

library_books

Improvements to PATRIC, the all bacterial Bioinformatics Database and Analysis Resource Center

2016
Nucleic Acids Res
PMCID: 5210524
PMID: 27899627
DOI: 10.1093/nar/gkw1017

[…] Bio () and Oxford Nanopore (,). PATRIC provides several assembly strategies (Figure ) that include algorithms for base calling correction [BayesHammer () and Kmergenie ()], and assemblers [Velvet (), IDBA (), Spades (), MEGAHIT () and MiniASM ()]. This is followed by scoring and two assembly evaluation frameworks, ALE () and a custom ARAST evaluation procedure. Finally, QUAST (,)—run at the end of […]

library_books

Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila

2016
PMCID: 5100859
PMID: 27633791
DOI: 10.1534/g3.116.033308

[…] The genome of M. psychrophila was sequenced using Illumina HiSequation 2000 apparatus. The data were assembled using release v0.19 of Idba (). We used homology and ab-initio prediction to identify protein-coding genes. For the homology-based gene prediction, we aligned the National Center for Biotechnology Information (NCBI) nr prot […]


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

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