De novo genes

[NGS_user]

Hi guys,
I am looking to sequence genes from a species with no reference genome I need to make a decent assembly has anyone got any advice or know of any pipelines that have been described for denovo assembly of genes and not full genomes.

[Torst]

Hi guys,
I am looking to sequence genes from a species with no reference genome I need to make a decent assembly has anyone got any advice or know of any pipelines that have been described for denovo assembly of genes and not full genomes.

If you sequence genomic DNA, you will have to assemble a genome. Perhaps you should sequence a transcriptome (RNA/cDNA) so you only get sequence reads for the genes?

[waterboy]

what kind of reads do you have? is it transcriptome data or genomic data?

[NGS_user]

Its genomic data. Thanks for the reply guys.

[NGS_user]

Anyone got any ideas? I am going to try some assemblers I found in the program list on this site but can anyone suggest alternate ways at all? Thank you in advance

[bioinfosm]

SOAP or velvet followed by something like glimmer to identify ORFS would get you started I suppose