Small Genome Mapping Assembly

Question

[Nicolas Rosewick]

Hi,

Can anyone suggest me a good small genome assembly with reference. My sequence are produced from sanger sequencing.

Thanks,

N.

[Pasta]

What kind of genome ?

[Nicolas Rosewick]

It's a virus genome so it's very small ~10kb

[Neilfws]

I assume you mean "assembler" not "assembly"? And by "reference" you mean literature, not a reference genome?

[Nicolas Rosewick]

Yes assembler sorry. And by reference I mean reference genome

Answer 1

[Martin A Hansen]

I suggest MIRA.

Answer 2

[Pierre Lindenbaum]

You could try Consed in http://www.phrap.org/phredphrapconsed.html . This tool was used during the SRAS outbreak: http://www.sciencemag.org/content/300/5624/1399.long

Answer 3

[Pasta]

You can try Edena, it is very accurate and easy to use (you dont have tons of tools to install). And the developer is very nice :)

Answer 4

[Lee Katz]

The AMOS package is really great for most things. Your question also depends on the chemistry you are using.

454 - Newbler continues to be the best at 454. Also, AMOScmp.

Illumina - Use Nesoni which is a nice wrapper around SHRiMP. Also, AMOScmp-shortReads

Answer 5

[Joseph Hughes]

This is a program we have developed at the CVR for assembling viral genomes: http://bioinformatics.cvr.ac.uk/Tanoti/index.php

It is specifically designed to map as many reads as possible and allows for quite a lot of variation relative to the reference.

Are your sequences in fastq format?