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.

RNASeqReadSimulator – A Simple RNA-Seq Read Simulator

RNASeqReadSimulator

:: DESCRIPTION

RNASeqReadSimulator is a set of scripts generating simulated RNA-Seq reads. RNASeqReadSimulator provides users a simple tool to generate RNA-Seq reads for research purposes, and a framework to allow experienced users to expand functions.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

  RNASeqReadSimulator

:: MORE INFORMATION

PALMapper 0.5 – Spliced Alignments of RNA-Seq Reads

PALMapper 0.5

:: DESCRIPTION

PALMapper, a fast and easy-to-use tool that is designed to accurately compute both unspliced and spliced alignments for millions of RNA-Seq reads. It combines the efficient read mapper GenomeMapper with the spliced aligner QPALMA, which exploits read-quality information and predictions of splice sites to improve the alignment accuracy.

::DEVELOPER

Rätsch Lab @ the Friedrich Miescher Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 PALMapper

:: MORE INFORMATION

Citation:

Jean, G., Kahles, A., Sreedharan, V.T., De Bona, F., Raetsch, G.,
RNA-Seq Read Alignments with PALMapper,
Curr. Protoc. Bioinform., 32:11.6.1-11.6.38, 2010.

Rcorrector – Error Correction for Illumina RNA-seq Reads

Rcorrector 1.0.1

:: DESCRIPTION

Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.

::DEVELOPER

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux
  • Perl

:: DOWNLOAD

 Rcorrector

:: MORE INFORMATION

Citation

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.
Song L, Florea L.
Gigascience. 2015 Oct 19;4:48. doi: 10.1186/s13742-015-0089-y.

MapSplice 2.1.8 – Mapping of RNA-seq reads for Splice Junction Discovery

MapSplice 2.1.8

:: DESCRIPTION

MapSplice is an algorithm for mapping RNA-seq data to reference genome for splice junction discovery.  MapSplice algorithm to detect splice junctions without any dependence on splice site features. This enables MapSplice to discover non-canonical junctions and other novel splicing events, in additional to the more common canonical junctions.

::DEVELOPER

Bioinformatics Lab @CS.UKy.edu

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 MapSplice

:: MORE INFORMATION

Citation

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.
Nucleic Acids Res, 38(18):e178, 2010.

MMSEQ 1.0.2 – Isoform Expression Estimation using Multi-mapping RNA-seq reads

MMSEQ 1.0.2

:: DESCRIPTION

MMSEQ deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms). The software can take into account non-uniform read generation and works with paired-end reads.

::DEVELOPER

Dr Ernest Turro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MMSEQ

:: MORE INFORMATION

Citation

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
Turro E, Su SY, Gonçalves Â, Coin LJ, Richardson S, Lewin A.
Genome Biol. 2011;12(2):R13. Epub 2011 Feb 10.

INSEGT 1.0 – Analyse Alignments of RNA-Seq reads using Gene Annotations

INSEGT 1.0

:: DESCRIPTION

INSEGT is a tool to analyse alignments of RNA-Seq reads (single-end or paired-end) by using gene annotations. It can measure exon, transcript and gene expression levels of given annotations. If read alignments span more than one exon, INSEGT can also compute possible exon combinations (tuple) and their expression levels. According to requirements it computes maximal tuple or tuple with a certain length. For paired-end reads INSEGT builds also tuple, whose exons are connected by matepairs. Briefly it searches the intervals of the read alignments in the intervals of the given annotations. It counts the mapped reads for each annotation and its parent annotation and stores the mapped annotations for each read.

::DEVELOPER

David Weese , Sabrina Krakau.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 INSEGT

:: MORE INFORMATION

ReadSpy – Assessment of Uniformity in RNA-Seq reads

ReadSpy

:: DESCRIPTION

ReadSpy is a free software for statistically addressing uniformity in reads from RNA-Seq experiment.

::DEVELOPER

Valerie Hower

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ReadSpy

:: MORE INFORMATION

Citation

V. Hower, R. Starfield, A. Roberts, and L. Pachter,
Quantifying uniformity in mapped reads