IDBA-Tran protocols

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chevron_left De novo transcriptome assembly Read alignment Error correction Known transcript quantification chevron_right
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IDBA-Tran specifications

Information


Unique identifier OMICS_01318
Name IDBA-Tran
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
GCC
Maintained Yes

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Maintainers


  • person_outline Francis Chin <>
  • person_outline Yu Peng <>

Additional information


The software is also available via Docker.

Publication for IDBA-Tran

IDBA-Tran in pipeline

2013
PMCID: 4053832
PMID: 23998801
DOI: 10.1186/gb-2013-14-8-310

[…] for efficient and accurate analysis of newly generated high-throughput data are continuing to be developed. henry cm leung (the university of hong kong, china) described a de novo rna-seq assembler, idba-tran, designed to remove assembly paths of de bruijn graphs associated with sequencing errors and for merging paths caused by polymorphisms. the algorithm achieved both better sensitivity (more […]


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IDBA-Tran in publications

 (13)
PMCID: 5511173
PMID: 28710480
DOI: 10.1038/s41598-017-05605-5

[…] (rrna removal; see refs and for details on transcriptome assembly). adapter and low quality sequences were trimmed, normalized, and assembled de novo into contigs with the assembler trinity or idba-tran, version 1.1.1 in case of w. argentea , ., homeodomain amino acid sequences of gbx, dlx, hox1, hox3, cdx, and lhx2/4 were retrieved from the homeobox database […]

PMCID: 5336659
PMID: 28259138
DOI: 10.1186/s12862-017-0904-4

[…] nucleotides have a phred score [, ] above 15 were kept for further analyses (additional file ). the processed (using cutadapt v.1.8.1 and condetri v.2.2) illumina reads were assembled de novo using idba-tran v.1.1.1 []. idba-tran assemblies are constructed using an initial k-mer size of 20, an iteration size of 5, and a maximum k-mer size of 120 (additional file )., assemblies were screened […]

PMCID: 5322684
PMID: 28250805
DOI: 10.1186/s13015-017-0091-2

[…] properly., most, if not all current short-read transcriptome assemblers are based on de bruijn graphs. among the best known are oases [], trinity [], and to a lesser degree trans-abyss [] and idba-tran []. common to all of them is the lack of a clear and explicit model for repeats in rna-seq data. heuristics are thus used to try and cope efficiently with repeats. for instance, in oases […]

PMCID: 5148890
PMID: 27938328
DOI: 10.1186/s12859-016-1406-x

[…] and a yeast) and two simulated datasets derived from metazoan reference genome annotations. all of these datasets were assembled using three currently popular assembly packages (clc, trinity and idba-tran). in addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. for all eight datasets our pipeline […]

PMCID: 5103448
PMID: 27832738
DOI: 10.1186/s12864-016-3080-9

[…] all downstream analyses were conducted with high-quality and clean libraries., the filtered short-read and long-read transcriptome libraries were reconstructed into contiguous cdna sequences with idba_tran v1.1.1 [] and mira4 [] software, respectively. information regarding the mrna sources is summarised in table . the short-read transcriptome assemblies with idba_tran were executed […]


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IDBA-Tran institution(s)
Department of Computer Science, The University of Hong Kong, Hong Kong; CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy Sciences, Shanghai, China
IDBA-Tran funding source(s)
Supported, in part, by RGC HKU 7111/12E and HKU 719709E, the Shanghai Pujiang Plan (Y057C11501) and Bill & Melinda Gates Foundation Project (‘‘C4 Rice’’).

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