IDBA-UD pipeline

IDBA-UD specifications

Information


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

 (19)
2017
PMCID: 5297240
PMID: 28176851
DOI: 10.1038/srep42189

[…] (gb) of paired-end reads were obtained for each sample, totalling 197.4 gb of high-quality data free of host genomic and adaptor contaminants., the illumina reads were assembled into contigs using idba-ud23 with default parameters. genes were predicted on the contigs with metagenemark24. a non-redundant gene catalogue was constructed with cd-hit25 using a sequence identity cut-off of 0.95, […]

2017
PMCID: 5315449
PMID: 28232956
DOI: 10.1126/sciadv.1602105

[…] on an illumina nextseq machine [2 × 75 base pairs (bp)], with 114 and 71 million pe reads recovered, respectively. reads from both libraries were pooled and assembled into contigs using the idba-ud program (40), resulting in 374,363 contigs (cumulated size, 580 mb; n50, 3783 bp; maximum size, 490 kb; mean size, 1402 bp). translated coding sequences resulting from this assembly [594,648 […]

2017
PMCID: 5334579
PMID: 28254972
DOI: 10.1128/genomeA.01670-16

[…] 301 bp paired-end chemistry. raw reads were preprocessed to remove adapter sequences and low-quality reads using trimmomatic (v0.36) software (3)., de novo assembly of the reads was performed using idba-ud genome assembler (v1.0.9) (4) that generated contig numbers between 24 and 46 per genome with a total size ranging from 2.37 mbp to 2.50 mbp. the g+c content ranged from 53.4% to 53.6%. […]

2017
PMCID: 5407278
PMID: 28462059
DOI: 10.7717/peerj.3269

[…] adapters and were filtered by quality (≥q20) and length (≥50 bp) using trimmomatic v0.32 (bolger, lohse & usadel, 2014). each library was assembled into contigs using 17,000,000 reads and idba-ud (peng et al., 2012), and normalized to the smallest library size (6,000 contigs) using seqtk (https://github.com/lh3/seqtk) (perner et al., 2014) (table s1 ). all contigs were searched […]

2017
PMCID: 5427200
PMID: 28495765
DOI: 10.1128/genomeA.00239-17

[…] and sequencing was carried out on an illumina miseq instrument, resulting in 1,214,756 paired-end reads (728,853.6 kb). quality trimming and de novo assembly were performed using trimmomatic and idba_ud software, respectively (5, 6), resulting in a complete genome sequence with a length of 35,203 bp, a g+c content of 51.94%, and an average coverage of 4,853× (1,058,791 reads). the assembly […]

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

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