Tag: RNA-Seq

NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python

:: DOWNLOAD

 NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

SNAPR – Scalable Nucleotide Alignment Program RNA-seq

SNAPR

:: DESCRIPTION

SNAPR is a new method for RNA-seq analysis, optimized for hundreds or even thousands of RNA-seq libraries. SNAPR reads from and writes to BAM format, automatically generates read counts, and accurately identifies viral/bacterial infections and gene fusions.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • C++

:: DOWNLOAD

 SNAPR

:: MORE INFORMATION

Flux Simulator 1.2.1 – Modeling RNA-Seq Experiments

Flux Simulator 1.2.1

:: DESCRIPTION

The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.

::DEVELOPER

Micha Sammeth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Flux Simulator

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.

OSA 4.1.1.1 – Alignment tool for RNA-Seq

OSA 4.1.1.1

:: DESCRIPTION

OSA (Omicsoft sequence aligner) is a fast and accurate alignment tool for RNA-Seq data.

::DEVELOPER

OmicSoft Corporation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/ MacOsX

:: DOWNLOAD

 OSA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.
OSA: a fast and accurate alignment tool for RNA-Seq.
Hu J, Ge H, Newman M, Liu K.

CracTools 1.24 / digitagCT 1.0.2 – Integrated pipelines for RNA-Seq Analysis using CRAC

CracTools 1.24 / digitagCT 1.0.2

:: DESCRIPTION

CracTools is a set of pipelines allowing to perform diverse RNA-Seq analysis such as chimeras detection, splicing variant detection, SNPs calling, and such.

The digitagCT distribution is part of the CracTools

::DEVELOPER

CracTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CracTools ,digitagCT

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Mar;42(5):2820-32. doi: 10.1093/nar/gkt1300. Epub 2013 Dec 18.
Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome.
Philippe N1, Bou Samra E, Boureux A, Mancheron A, Rufflé F, Bai Q, De Vos J, Rivals E, Commes T.

EBARDenovo 2.0.1 – Highly-accurate de novo Assembler of Paired-end RNA-Seq

EBARDenovo 2.0.1

:: DESCRIPTION

EBARDenovo is a highly-accurate search-based de novo assembler of paired-end RNA-Seq for advance transcriptomic study.

::DEVELOPER

Frank Hsueh-Ting Chu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX

:: DOWNLOAD

 EBARDenovo

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1004-1010. Epub 2013 Mar 1.
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY.

SplAdder 2.4.0 – Detection and Quantification of Alternative Splicing Events from RNA-Seq data

SplAdder 2.4.0

:: DESCRIPTION

SplAdder is the short form of Splice Adder and describes a tool that augments a given annotation of a genome based on evidence from RNA-Seq alignment data.

::DEVELOPER

Rätsch Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Python
  • MatLab

:: DOWNLOAD

  SplAdder

:: MORE INFORMATION

Citation

SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data.
Kahles A, Ong CS, Zhong Y, Rätsch G.
Bioinformatics. 2016 Feb 11. pii: btw076.

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.

Net-RSTQ – Network-based method for RNA-Seq-based Transcript Quantification

Net-RSTQ

:: DESCRIPTION

Net-RSTQ is a software to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation.

::DEVELOPER

KUANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 Net-RSTQ

:: MORE INFORMATION

Citation

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.
Zhang W, Chang JW, Lin L, Minn K, Wu B, Chien J, Yong J, Zheng H, Kuang R.
PLoS Comput Biol. 2015 Dec 23;11(12):e1004465. doi: 10.1371/journal.pcbi.1004465.