Aligning de-novo assembly to reference strain genome

Question

[aindap]

Dear Biostars Community -

I generated a de-novo assembly of my viral strain. I wanted to analyze differences of my denovo result to a reference strain, so got a very useful report from Assemblytics in conjunction with using the nucmer program from MUMmer. However the output of the alignment is in the delta format. There is delta-filterprogram to manipulate the alignment. But what I really want to do is ailgn my de-novo to the reference and have the alignment in FASTA for MAF format. The size of genome is fairly modest ( < 200kb) I was thinking of using mafft. Are there any other alignment programs that might be more appropriate?

Answer 1

[Petr Ponomarenko]

You may use mVISTA http://genome.lbl.gov/vista/mvista/submit.shtml or ask Inna Dubchak directly

Answer 2

[vmicrobio]

I would use stampy or bowtie2 alignment tools

Answer 3

[asur]

I actually had the same issue with nucmer. I would say Mauve is the best tool for multi-genome/assembly alignment, since it's fast and has it's own viewer. If you wanted an alignment in FASTA or MAF, mafft does a good job when there are chromosome length scaffolds, but if there are contigs spanning portions of chromosomes, I found it to struggle quite a bit. kAlign did a much better job when you don't penalize end gaps for those "floating" contigs. Mugsy uses nucmer to produce a MAF file.