QC: FastQC

Mapping: STAR universal RNA-seq aligner

Denovo Assembly: Velvet de novo assembler

Transcriptome analysis: featureCounts followed by Limma/Voom

Cheers,

Leon

Have a look at this link:

http://seqanswers.com/wiki/Software/list

and the mini description here:

http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29

de novo assembly: Velvet

Alingment of RNAseq to genome: Tophat2, Bowtie2, Cufflinks

y donot use trial version of CLC genomics work bench if your able to analyse your data using Trial version just mail me at [email protected] we also have licence for CLC workbench you can access it

How about these tools?

They seem pretty good too:

http://www.genecodes.com/download/external-tools-download

Best wishe,

Nikos

Take a look at Trinity

Very good for de novo assembly of transcriptomes  and many scripts for post-analyses.

But you need access to some powerful computer.

Best

Galaxy  you can try one of the several free online servers

You can use R with free packages available from bioconductor.

http://master.bioconductor.org/help/workflows/high-throughput-sequencing/ 

There is also a new one for assembly, that just published a paper for that on nature and called stringtie. It seems that you get better results than the cufflinks.

http://ccb.jhu.edu/software/stringtie/

You can try IGV

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

http://www.broadinstitute.org/igv/home

QC -  FastQC/Trimmomatic

Denovo assembly -  SPAdes +QUAST

Mapping -  Boutie2/BWA/Contiguator

Annotation - RAST/Glimmer/Genmark

Variation analysis - Mauve

Thank you to all for your valuable reply

Try REVIGO or DAVID - tools with very friendly interface.

can visit http://bioinformaticssoftwareandtools.co.in/ngs.php#trans_table

You may try Gene Codes as it has a good package and free

http://www.genecodes.com/sequencher-features/next-gen-sequencing

Hi Nandu,

I would recommend galaxy (https://usegalaxy.org/). It is is an open source, web-based platform for NGS data analysis which includes RNAseQ, DNA sequencing data and SNP calling etc. It integrates several widely used tools for NGS data analysis using which you can develop your own pipeline for analysis. All you need is to create a login on its web interface. All the best.

You can use CSI NGS Portal for free online NGS data analysis without sign up/login requirement !

https://www.preprints.org/manuscript/201910.0146/v1