Tag: Transcriptome

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.

est2assembly 1.13 – Assembly and Annotation of Transcriptomes for any Species

est2assembly 1.13

:: DESCRIPTION

The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.

::DEVELOPER

Dr Alexie Papanicolaou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 est2assembly

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Dec 24;10:447. doi: 10.1186/1471-2105-10-447.
Next generation transcriptomes for next generation genomes using est2assembly.
Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG.

Scripture Beta2 – Transcriptome Reconstruction

Scripture Beta2

:: DESCRIPTION

Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

:DEVELOPER

Scripture Team

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Scripture

:: MORE INFORMATION

Citation:

Mitchell Guttman et al.
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Nature Biotechnology 28, 503–510 (2010)