Assembly with Reference Sequence

[Daniel Fernandez]

Hi, anybody can tell me about one program to assembly with a reference sequence (in Linux)
I use CAP3 but this can't use a reference sequence.

Well I need assembly more than 300 million, so I prefer a command program like CAP3
Or I can use other program (blast) to choose the best reads (less 500) and then assembly this hits with a reference sequences with a graphic program.

I've been looking but no luck.

[fahmida]

What is your sequencing platform? assuming illumina you can use Velvet's Columbus module as suggested by:

http://seqanswers.com/forums/showthread.php?t=17577

[sklages]

Hi, anybody can tell me about one program to assembly with a reference sequence (in Linux)
I use CAP3 but this can't use a reference sequence.

Well I need assembly more than 300 million, so I prefer a command program like CAP3
Or I can use other program (blast) to choose the best reads (less 500) and then assembly this hits with a reference sequences with a graphic program.

I've been looking but no luck.

Not much information you provide :-)
type of input material? type of data? type of reference?

Have a look at http://seqanswers.com/wiki/Software to get idea of what software might be doing the job for you. There are numerous mappers (assuming you refer to mappping).

[Daniel Fernandez]

Well, this is the link, it is 454 (http://www.ncbi.nlm.nih.gov/sra/SRX172665).
This genome is in SRA and I converted to fastq and then fasta. My reference sequences are genes in fasta.
I'm trying with Velvet thanks for the recommendation, if anymore have other sugestion, thanks.