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iAssembler specifications

Information


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
Requirements
BioPerl
Maintained Yes

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Maintainer


  • person_outline Zhangjun Fei <>

Publication for iAssembler

iAssembler in pipelines

 (7)
2018
PMCID: 5799245
PMID: 29402924
DOI: 10.1038/s41598-018-20548-1

[…] containing poly n and sequences <50 bp) using fastqc tools v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). the de novo assembly of high quality reads was performed using iassembler v1.0 (beta) (http://bioinfo.bti.cornell.edu/tool/-iassembler/). the assembled unigenes were annotated against non-redundant (nr) protein database through blastx with e-value cut-off […]

2015
PMCID: 4620235
PMID: 26543846
DOI: 10.1155/2015/527054

[…] c. oleifera, respectively [, ]. the significantly greater number of sequences we obtained for these two species may be because newbler performs best for restoring full-length transcripts [, ], but iassembler can identify incorrectly assembled contigs and should be more conservative []. moreover, the greater number of sequences for c. azalea was much more than the other two species and may […]

2013
PMCID: 3564996
PMID: 23390612
DOI: 10.1534/g3.112.003871

[…] (). mira produced identical duplicate contigs in areas with high read depth, and these were merged using additional iterations of both mira and cap3 () at 97% minimum similarity, using the pipeline iassembler v1.3 (). successful resolution of highly similar alleles and/or paralogs into unique contigs was verified by examining synonymous site divergence among gene family members using […]

2013
PMCID: 3832898
PMID: 24112713
DOI: 10.1186/1471-2164-14-697

[…] to remove reads containing low complexity sequence, reads shorter than 100bp, and to clip low quality read ends (ends rich in undetermined bases). 454 reads were assembled into contigs de-novo using iassembler v1.3 []. contigs were searched for di, tri, and tetra microsatellites of five repeats or more using phobos v3.3.12 as implemented in geneious v5.5.3 []. illumina hiseq reads were aligned […]

2012
PMCID: 3472759
PMID: 23109867
DOI: 10.3390/ijms130911497

[…] and excluded. the resulting high quality grape ests have been deposited in genbank dbest database under accession numbers jk266423 to jk266914., the ests were assembled into unigenes using iassembler [] with minimum overlap of 40 bp and minimum percent identity of 97. the resulting grape unigene sequences were compared against genbank non-redundant (nr) and uniprot [] protein databases […]


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iAssembler in publications

 (40)
PMCID: 5799245
PMID: 29402924
DOI: 10.1038/s41598-018-20548-1

[…] containing poly n and sequences <50 bp) using fastqc tools v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). the de novo assembly of high quality reads was performed using iassembler v1.0 (beta) (http://bioinfo.bti.cornell.edu/tool/-iassembler/). the assembled unigenes were annotated against non-redundant (nr) protein database through blastx with e-value cut-off […]

PMCID: 5738619
PMID: 29111565
DOI: 10.1590/1678-4685-GMB-2017-0053

[…] 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 […]

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

[…] 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., […]

PMCID: 5814581
PMID: 28850773
DOI: 10.1111/pbi.12823

[…] libraries were sequenced on an ion torrent pgm at life sequencing (valencia, spain). sequence quality trimming, de novo assembly and posterior analysis were conducted using custom python scripts and iassembler software (zheng et al., ). unigenes composed of at least two members were used for library comparison by blastn using the blast user db tool at http://nbc11.biologie.uni-kl.de/., […]

PMCID: 5397871
PMID: 28425468
DOI: 10.1038/srep46163

[…] 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 […]


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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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