Agalma 1.0.0 – A Transcriptome Assembly and Phylogenetic Analysis Environment

Agalma 1.0.0

:: DESCRIPTION

Agalma is an automated tool that constructs matrices for phylogenomic analyses.  It builds alignments of homologous genes and preliminary species trees from genomic and transcriptome data.

::DEVELOPER

The Dunn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Agalma

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 19;14:330. doi: 10.1186/1471-2105-14-330.
Agalma: an automated phylogenomics workflow.
Dunn CW1, Howison M, Zapata F.

CBrowse 1.11 – SAM/BAM-based Contig Browser for Transcriptome Assembly

CBrowse 1.11

:: DESCRIPTION

CBrowse (Contig Browser) is a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.  It takes the contig sequence file and its relevant SAM/BAM file as the input, processes the input data, detects polymorphisms and repeats, and generates image, JSON and MySQL-compatible text files that can be directly utilized by different viewers of CBrowse.

::DEVELOPER

Liang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CBrowse

:: MORE INFORMATION

Citation:

Pei Li, Guoli Ji, Min Dong, Emily Schmidt, Douglas Lenox, Liangliang Chen, Qi Liu, Lin Liu, Jie Zhang and Chun Liang (2012)
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Bioinformatics, doi: 10.1093/bioinformatics/bts443

IsoLasso 2.6.1 – A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

IsoLasso 2.6.1

:: DESCRIPTION

IsoLasso is an algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab
  • C Compiler

:: DOWNLOAD

  IsoLasso

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1693-707. doi: 10.1089/cmb.2011.0171. Epub 2011 Sep 27. IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. Li W1, Feng J, Jiang T.

MaLTA – Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq data

MaLTA

:: DESCRIPTION

MaLTA is a method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data.

::DEVELOPER

Georgia State University NGS Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 MaLTA

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Jul 14;15 Suppl 5:S7. doi: 10.1186/1471-2164-15-S5-S7. Epub 2014 Jul 14.
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data.
Mangul S, Caciula A, Al Seesi S, Brinza D, M?ndoiu I, Zelikovsky A.