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iAssembler specifications


Unique identifier OMICS_19115
Name iAssembler
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A EST sequence file and optionally the corresponding sequence quality file.
Input format FASTA
Output data Generates five files and a "log" folder: Unigene sequences generated from the EST assembly process, a file containing the alignment information of each sequence read to its corresponding unigene, a file containing unigenes and their corresponding EST members, a file containing the mapping details of EST members to their corresponding unigenes, a file containing the summary statistics of aligning ESTs to their corresponding unigenes, and a folder containing all the log files from the program.
Output format FASTA, SAM, TSV
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.3.3
Stability Stable
Maintained Yes


No version available


  • person_outline Zhangjun Fei

Publication for iAssembler

iAssembler citations


Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight and Arn) under drought stress

Sci Rep
PMCID: 5799245
PMID: 29402924
DOI: 10.1038/s41598-018-20548-1

[…] e to accuracy, rapidity and low cost, its use has also been extended to unearth the unique genetic characteristics in the non-model plant systems. The sequences generated were de novo assembled using iAssembler software. The iAssembler generates initial assemblies by MIRA and CAP3 assemblers and makes correction in two common types of transcriptome assembly errors: i) ESTs from different transcrip […]


Transcriptome sequencing analysis of alfalfa reveals CBF genes potentially playing important roles in response to freezing stress

Genet Mol Biol
PMCID: 5738619
PMID: 29111565
DOI: 10.1590/1678-4685-GMB-2017-0053
call_split See protocol

[…] raw sequences to produce clean data. Then, clean reads were merged and assembled de novo into contigs using Trinity with default parameters (). The contigs were further clustered into unigenes using iAssembler () and CD-HIT-EST (). To evaluate their genetic information, these assembled unigenes were BLAST-searched against alfalfa unigenes reported by using the BLASTN program and an E-value set a […]


Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans

Sci Rep
PMCID: 5648782
PMID: 29051502
DOI: 10.1038/s41598-017-13176-8

[…] re filtered out using custom perl scripts (VecScreenFilter.pl, compare_2Files.pl, bad_data_uniq.pl; available upon request) and seqtk (https://github.com/lh3/seqtk, accessed Oct 8, 2014). Afterwards, iAssembler tool (v1.3.2.) (-a 10 -b 10 –d) was used to cluster and assembly contigs to obtain unigene sequences. Raw sequence reads can be found in the SRA database under BioProject PRJNA401426. […]


Transcriptome Analysis of Mango (Mangifera indica L.) Fruit Epidermal Peel to Identify Putative Cuticle Associated Genes

Sci Rep
PMCID: 5397871
PMID: 28425468
DOI: 10.1038/srep46163

[…] were removed or trimmed from the contigs using SeqClean (https://sourceforge.net/projects/seqclean/). To remove redundancies in the contigs, the remaining contigs were further de novo assembled using iAssembler with 97% minimum percent identify.The final assembled mango unigenes were used to query the UniProt (Swiss-Prot and TrEMBL; http://www.uniprot.org/) and Arabidopsis protein databases (https […]


Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids

PMCID: 5333554
PMID: 28265493
DOI: 10.7717/peerj.2938

[…] ve in merging reads, resulting in a high number of redundant short contigs but fewer chimeric contigs (). This appeared to be the case for the root transcriptome in which the 190,269 transcripts from iAssembler pipeline were significantly reduced to 26,301 proportionally longer transcripts () when constructed with Trinity pipeline using the simulated Illumina reads (). The comparison between the i […]


Complete Genome Sequences of the Neethling Like Lumpy Skin Disease Virus Strains Obtained Directly from Three Commercial Live Attenuated Vaccines

Genome Announc
PMCID: 5105100
PMID: 27834707
DOI: 10.1128/genomeA.01255-16

[…] sing the Long_Amplicon_Analysis protocol (default parameters; Pacific Biosciences) in SMRT Portal version 2.3.0 (Pacific Biosciences). These amplicons were further assembled into unique contigs using iAssembler software (). Discrepancies with previously published LSDV genomes were confirmed by Sanger sequencing. The protein-coding genes were predicted by NCBI ORF-Finder (http://www.ncbi.nlm.nih.go […]


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iAssembler institution(s)
Department of Ornamental Horticulture, China Agricultural University, Beijing, China; Boyce Thompson Institute, Cornell University, Ithaca, NY, USA; USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
iAssembler funding source(s)
Supported by National Science Foundation grant (IOS-0923312, IOS-1110080) and the United States-Israel Binational Agricultural Research and Development Fund (IS-3877-06).

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