Multiple whole genomes alignment

[bio_73]

Hello,
I'm a newbie
I have to align 5 whole chloroplast genomes de novo assembled with Soap2Denovo.
Each genome is a multifasta file with both contigs and scaffolds.
Some softwares needs to have for each genome a fasta file with only one sequence: can i obtain a fasta file with only one sequence merging alle scaffolds and contings?
Thanks

[Brian Bushnell]

You can do that, but the result would be junk, so I don't recommend it. It's not entirely clear to me what you are trying to accomplish, though.

[bio_73]

You can do that, but the result would be junk, so I don't recommend it. It's not entirely clear to me what you are trying to accomplish, though.

I have 5 chloroplast genomes of close related species and i have to align to a reference genome to find private Snp' in each genome.
My aim is to find a set of snp in genomes that discriminates between species.

[Brian Bushnell]

OK, you can do that by aligning the chloroplast genomes to the reference without merging anything. For example, with BBMap:

bbmap.sh ref=reference.fasta

bbmap.sh in=chloro1.fasta out=chloro1.sam
bbmap.sh in=chloro2.fasta out=chloro2.sam
...etc.

Then you can call SNPs with samtools or something, with respect to coordinates on the reference.

[juan.isaza]

You can use MUMmer, it allows to compare draft genomes in multifasta format. There is also a pipeline with MUMmer to identify SNPs.

Check the manual ----> http://mummer.sourceforge.net/manual/#aligningdraft