Contig_Analysis

[pari_89]

Hi everyone, I have used a series of de-novo tools and generated contigs from each one of them. I have used QUAST to assess the quality of assembly but QUAST does not display alignments which I would like to see.

I have also done the same with reference tools including Mira, CLCworkbench and Newbler.

Can anyone tell me how can I assess the quality of the reference-guided assemblies and which tool is good?


Thank you

Kind Regards

Parinita.

[flxlex]

Check out http://flxlexblog.wordpress.com/2013...athon2-debate/ :-)

[pari_89]

Check out http://flxlexblog.wordpress.com/2013...athon2-debate/ :-)

Hi thanks a lot. I was not aware of those tools. I wanted to try some of them but the problem is that the only file that my assemblers produce in common are contigs. CLC has its own viewer, RAy does not produce sam files, Newbler produce ACE files.

I need an equal platform to assess the assemblies. I am currently using comparative genomics for this but would like some more input or ideas please?

Thank you.