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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 |
Versioning
No version available
Maintainer
- person_outline Zhangjun Fei
Publication for iAssembler
IAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences.
iAssembler citations
(40)Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight and Arn) under drought stress
[…] 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
[…] 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
[…] 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
[…] 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
[…] 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
[…] 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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