:: DESCRIPTION
PipeMeta is a perl script designed to assist in running an annotation pipeline for 454 transcriptome projects.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
LR50 is a pipeline for assessing the quality of insect transcriptomes which generated by sequencing technology.
::DEVELOPER
Li Lab: Insect Genomic and Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
VTBuilder is a tool for the inference of non-chimeric contigs from read data that has been sequenced from complex multi-isoformic transcriptomes, such as snake venom glands, or rapidly evolving viral populations, such as HIV-1.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 Dec 3;15(1):389.
VTBuilder: a tool for the assembly of multi isoform transcriptomes.
Archer JP, Whiteley G, Casewell NR, Harrison RA, Wagstaff SC.
:: DESCRIPTION
NGS-Trex is an automatic system for the analysis of NGS-Seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013;14 Suppl 7:S10. doi: 10.1186/1471-2105-14-S7-S10. Epub 2013 Apr 22.
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer.
Boria I1, Boatti L, Pesole G, Mignone F.
:: DESCRIPTION
oposSOM translates microarray expression data into metadata of reduced dimension.
::DEVELOPER
Henry Wirth <wirth at izbi.uni-leipzig.de> and Martin Kalcher <mkalcher at porkbox.net>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on Bioconductor.
L?ffler-Wirth H, Kalcher M, Binder H.
Bioinformatics. 2015 Jun 10. pii: btv342
:: DESCRIPTION
Dissect (DIScovery of Structural Alteration Event Containing Transcripts) is a transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.
::DEVELOPER
Lab for Bioinformatics and Computational Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC
Dissect: detection and characterization of novel structural alterations in transcribed sequences
Bioinformatics. 2012 Jun 15;28(12):i179-87
:: DESCRIPTION
CEM is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Nov 15;28(22):2914-21. doi: 10.1093/bioinformatics/bts559. Epub 2012 Oct 11.
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
Li W1, Jiang T.
:: DESCRIPTION
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Annocript: a flexible pipeline for the annotation of transcriptomes also able to identify putative long noncoding RNAs.
Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R.
Bioinformatics. 2015 Feb 19. pii: btv106.
:: DESCRIPTION
PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. Unlike conventional methods that analyze each sample separately and then merge the outcomes to create a unified set of meta-annotations, PsiCLASS takes a multi-sample approach, simultaneously analyzing all RNA-seq data sets in an experiment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Song L, Sabunciyan S, Yang G, Florea L.
A multi-sample approach increases the accuracy of transcript assembly.
Nat Commun. 2019 Nov 1;10(1):5000. doi: 10.1038/s41467-019-12990-0. PMID: 31676772; PMCID: PMC6825223.
:: DESCRIPTION
Oqtans is an integrative online platform for quantitatively analyzing RNA-Seq experiments. It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis
::DEVELOPER
the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.
Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G.
Bioinformatics. 2014 May 1;30(9):1300-1. doi: 10.1093/bioinformatics/btt731.
