IDBA-UD protocols

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IDBA-UD specifications

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Unique identifier OMICS_01423
Name IDBA-UD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for IDBA-UD

IDBA-UD in pipelines

 (63)
2018
PMCID: 5796750
PMID: 29422788
DOI: 10.5423/PPJ.NT.08.2017.0190

[…] san diego). further image analysis and base calling were performed with real time analysis (rta) 2.7.3 and bcl2fastq v2.17.1.14 (illumina, inc., san diego). normalized reads were assembled using idba-ud ver. 1.1.1. () and contigs were aligned to the ncbi nucleotide database using blastn with an e-value cutoff of 1e-10. alignment results were classified taxonomically using krona tools (). […]

2018
PMCID: 5797428
PMID: 29434576
DOI: 10.3389/fmicb.2018.00028

[…] genome consisted of two contiguous, overlapping contigs of 1580543 kb and 15533 kb, respectively. the resulting assembly was compared to a previous version of the genome bin we had obtained by using idba-ud and newbler for assembly, and differential coverage binning on ∼150 nt reads from five runs of iontorrent sequencing (use of gc% and reads coverage from iontorrent pgm reads) (; ). the new […]

2018
PMCID: 5827749
PMID: 29483539
DOI: 10.1038/s41598-018-21919-4

[…] cleaned and quality filtered using trimmomatic. reads were then corrected for errors through string graph assembler which utilizes a k-mer centric algorithm. de novo assembly was attempted through idba-ud algorithm centred on de bruijn graph approach. genome annotation was carried out using the ncbi ‘prokaryotic genome annotation pipeline’. genomic context was visualized through gview. […]

2018
PMCID: 5852087
PMID: 29540736
DOI: 10.1038/s41598-018-22617-x

[…] mean quality. all reads with non-iupac characters were discarded as well as reads containing more than three ns., all reads which passed the quality assessment were pooled and cross-assembled with idba_ud version 1.1.1 with standard parameters. all contigs, which contained more than 90% of a single base, more than 90% gc or at, or which contained 50 or more bases of the same type in a row, […]

2018
PMCID: 5893878
PMID: 29636439
DOI: 10.1128/mBio.00441-18

[…] prior studies analyzed, referred to as nih2 () and nih3 (). all raw sequencing reads were trimmed using sickle (https://github.com/najoshi/sickle). each metagenome was assembled separately using idba_ud (). open reading frames (orfs) were predicted using prodigal () with the option to run in metagenome mode. predicted protein sequences were annotated based on usearch (–ublast) (, ) searches […]


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IDBA-UD in publications

 (235)
PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] pipeline, the reads first undergo adapter and quality trimming with trimmomatic [], then error correction with the sga k-mer correction algorithm []. next the corrected reads are assembled with the idba-ud algorithm []. some templates resulted in two or more assembled sequences (scaffolds 0-4). the script provided in additional file  was used to identify assembled sequences with only a scaffold […]

PMCID: 5911951
PMID: 29713376
DOI: 10.1186/s13068-018-1121-0

[…] of the five enrichment cultures (additional file ). specifically, pooled metagenomic clean reads from different time points of the same enrichment culture (additional file ) were co-assembled using idba-ud [] with a maximum k-mer size of 100 and a minimum contig length of 800 bp. open reading frames (orfs) of the assembled contigs were predicted using prodigal v2.60 [] in metagenome mode. […]

PMCID: 5924556
PMID: 29659545
DOI: 10.3390/genes9040214

[…] data were obtained after sequencing adapters, and reads with ambiguous n base or average base quality score less than 15 were removed from raw data. de novo metagenome assembly was performed with idba-ud (v1.1.1) [] for each sample, and reads were assembled with a series of different k-mer size (25–115 bp) in parallel, and then were mapped back to each of the assembled contigs for validation. […]

PMCID: 5923486
PMID: 29652800
DOI: 10.3390/v10040192

[…] host cell reads were removed using the fastq screen algorithm (available at http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) and fmdv reads assembled de novo into contigs with idba-ud and using a range of kmers []. only contigs which matched the fmdv library after running a basic local alignment search tool (blast) algorithm [] were assembled into consensus sequences using […]

PMCID: 5904459
PMID: 29696004
DOI: 10.3389/fmicb.2018.00680

[…] e-value of 1e-5, a minimum sequence identity of 60%, and a minimum alignment length of 15 amino acids (aa) was used., de novo metagenomic assemblies were generated with the uneven depth assembler idba-ud (). minimal contig length was set to 1000 bp and k-mers were iterated between 21 and 91 in steps of 20. descriptive statistics on metagenome sequence data and assemblies are provided […]


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IDBA-UD institution(s)
Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong

IDBA-UD review

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lille my

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Desktop
Quit accurate, not very easy to use