CStone – de novo Transcriptome Assembler

CStone

:: DESCRIPTION

CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric.

::DEVELOPER

John Archer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

CStone

:: MORE INFORMATION

Citation

Linheiro R, Archer J.
CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.
PLoS Comput Biol. 2021 Nov 23;17(11):e1009631. doi: 10.1371/journal.pcbi.1009631. Epub ahead of print. PMID: 34813594.

TimesVector 1.5 – Analysis of Time Series Transcriptome data from multiple Phenotypes

TimesVector 1.5

:: DESCRIPTION

TimesVector is a triclustering tool for clustering time-series data that comprises multiple conditions, or phenotypes.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

TimesVector

:: MORE INFORMATION

Citation

Jung I, Jo K, Kang H, Ahn H, Yu Y, Kim S.
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes.
Bioinformatics. 2017 Dec 1;33(23):3827-3835. doi: 10.1093/bioinformatics/btw780. PMID: 28096084.

TERA-Seq – True end-to-end Sequencing of native RNA molecules for Transcriptome Characterization

TERA-Seq

:: DESCRIPTION

TERA-Seq (True End-to-end RNA Sequencing) is a platform that addresses these limitations, permitting more thorough transcriptome characterization.

::DEVELOPER

Z. MOURELATOS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TERA-Seq

:: MORE INFORMATION

Citation

Ibrahim F, Oppelt J, Maragkakis M, Mourelatos Z.
TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization.
Nucleic Acids Res. 2021 Aug 24:gkab713. doi: 10.1093/nar/gkab713. Epub ahead of print. PMID: 34428294.

Flux Capacitor 1.6.1 – Quantify Expressed Sequence Features from Transcriptome

Flux Capacitor 1.6.1

:: DESCRIPTION

The Flux Capacitor is a program to quantify expressed sequence features (e.g., genes or transcripts) from transcriptome interrogations by short read sequencing.

::DEVELOPER

Micha Sammeth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Flux Capacitor

:: MORE INFORMATION

Citation

Nature. 2010 Apr 1;464(7289):773-7. doi: 10.1038/nature08903. Epub 2010 Mar 10.
Transcriptome genetics using second generation sequencing in a Caucasian population.
Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET.

miRDeep-P 1.3 / miRDP2 1.1.5 – Analyzing the microRNA Transcriptome in Plants

miRDeep-P 1.3 / miRDP2 1.1.5

:: DESCRIPTION

miRDeep-P (miRDP)  is a tool which can be used to detecting miRNAs in plants from deeply sequenced small RNA libraries. It was developed by modifying miRDeep, which is based on a probabilistic model of miRNA biogenesis in animals, with a plant-specific scoring system and filtering criteria.

miRDP2 is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm.

::DEVELOPER

Yang lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

 miRDeep-P / miRDP2 

:: MORE INFORMATION

Citation

Kuang Z, Wang Y, Li L, Yang X.
miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.
Bioinformatics. 2019 Jul 15;35(14):2521-2522. doi: 10.1093/bioinformatics/bty972. PMID: 30521000.

Bioinformatics. 2011 Sep 15;27(18):2614-5. doi: 10.1093/bioinformatics/btr430. Epub 2011 Jul 19.
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.
Yang X1, Li L.

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1 – Gene Fusion Discovery using Whole Genome and Transcriptome data

INTEGRATE 0.2.6 / INTEGRATE-Neo 1.2.1

:: DESCRIPTION

INTEGRATE is a tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.

INTEGRATE-Neo is a tool for gene fusion neoantigen discovering tool using next-generation sequencing data.

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

INTEGRATE / INTEGRATE-Neo

:: MORE INFORMATION

Citation

Zhang J, Mardis ER, Maher CA.
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.
Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674. PMID: 27797777; PMCID: PMC5408800.

Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA.
INTEGRATE: gene fusion discovery using whole genome and transcriptome data.
Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PMID: 26556708; PMCID: PMC4691743.

L_RNA_scaffolder – Long Transcriptome Reads to Scaffold Genome

L_RNA_scaffolder

:: DESCRIPTION

L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments.

::DEVELOPER

L_RNA_scaffolder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 L_RNA_scaffolder

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Sep 8;14:604. doi: 10.1186/1471-2164-14-604.
L_RNA_scaffolder: scaffolding genomes with transcripts.
Xue W1, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW.

TranscriptSimulator 0.7 – Simulate Transcriptome Next-gen Reads, including 454 and Illumina

TranscriptSimulator 0.7

:: DESCRIPTION

TranscriptSimulator: Simple text-based, next-gen output simulator. Specifically designed to simulate transcriptome next-gen reads, including 454 and Illumina. Uses a model to simulate transcription followed by simulated sequencing using various customizable parameters. Uses a nucleotide gene set as a template (e.g. in silico predicted gene set). Version 0.70 has simulated SNPs/Indels with an improved model.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 TranscriptSimulator

:: MORE INFORMATION