SSP – de novo Transcriptome Assembler

SSP

:: DESCRIPTION

SSP is a de novo transcriptome assembler that assembles RNA-seq reads into transcripts. SSP aims to reconstructs all the alternatively spliced isoforms and estimates the expression level of them.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux

:: DOWNLOAD

 SSP

:: MORE INFORMATION

TRAPID 2.0 – Rapid Analysis of Transcriptome Data

TRAPID 2.0

:: DESCRIPTION

TRAPID is an online tool for the fast, reliable and user-friendly analysis of de novo transcriptomes

::DEVELOPER

Comparative Network Biology – Vandepoele lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.
Van Bel M, Proost S, Van Neste C, Deforce D, Van de Peer Y, Vandepoele K.
Genome Biol. 2013 Dec 13;14(12):R134. doi: 10.1186/gb-2013-14-12-r134.

Rnnotator 3.5.0 – de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads

Rnnotator 3.5.0

:: DESCRIPTION

Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.

::DEVELOPER

Zhong Wang at U.S. Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl
  • Blat

:: DOWNLOAD

  Rnnotator

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:663. doi: 10.1186/1471-2164-11-663.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.

Scallop v0.10.4 – Reference-based Transcriptome Assembler for RNA-seq

Scallop v0.10.4

:: DESCRIPTION

Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviation minimization.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Boost

:: DOWNLOAD

Scallop

:: MORE INFORMATION

Citation

Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020.
Accurate assembly of transcripts through phase-preserving graph decomposition.
Shao M, Kingsford C.

m6Apred – Identification and Analysis of the N6-methyladenosine in Saccharomyces Cerevisiae Transcriptome

m6Apred

:: DESCRIPTION

The web-server m6Apred was developed to identify the N6-methyladenosine (m6A).

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome.
Chen W, Tran H, Liang Z, Lin H, Zhang L.
Sci Rep. 2015 Sep 7;5:13859. doi: 10.1038/srep13859.

DETONATE 1.11 – DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

DETONATE 1.11

:: DESCRIPTION

DETONATE consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.

::DEVELOPER

Colin Dewey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DETONATE

:: MORE INFORMATION

Citation

Genome Biol. 2014 Dec 21;15(12):553. doi: 10.1186/s13059-014-0553-5.
Evaluation of de novo transcriptome assemblies from RNA-Seq data.
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN.

BinPacker 1.1 – Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

BinPacker 1.1

:: DESCRIPTION

BinPacker is a novel de novo assembler by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems.

::DEVELOPER

BinPacker team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BinPacker

:: MORE INFORMATION

Citation

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data.
Liu J, Li G, Chang Z, Yu T, Liu B, McMullen R, Chen P, Huang X.
PLoS Comput Biol. 2016 Feb 19;12(2):e1004772. doi: 10.1371/journal.pcbi.1004772.

TCW 1.3.9 – Transcriptome Computational Workbench

TCW 1.3.9

:: DESCRIPTION

TCW is a software package for assembling, annotating, querying, and comparing transcript and expression level data.

::DEVELOPER

Arizona Genomics Computational Lab (AGCoL)

:: SCREENSHOTS

TCW

:: REQUIREMENTS

  • Linux / MacOSX /Windows
  • Java

:: DOWNLOAD

 TCW

:: MORE INFORMATION

Citation:

PLoS One. 2013 Jul 17;8(7):e69401. doi: 10.1371/journal.pone.0069401. Print 2013.
TCW: transcriptome computational workbench.
Soderlund C1, Nelson W, Willer M, Gang DR.

TransPS 1.1.0 – Transcriptome Post Scaffolding

TransPS 1.1.0

:: DESCRIPTION

TransPS is a pipeline for post-processing of pre-assembled transcriptomes using reference based method.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TransPS

:: MORE INFORMATION

Citation

A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs,
Computational Biology Journal, vol. 2014, Article ID 961823, 4 pages, 2014. doi:10.1155/2014/961823
Mingming Liu, Zach N. Adelman, Kevin M. Myles, and Liqing Zhang

Oqtans 0.1 beta – Online Quantitative Transcriptome Analysis

Oqtans 0.1 beta

:: 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

Rätsch Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Oqtans

:: 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.