Question: Aligning de-novo assembly to reference strain genome
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gravatar for aindap
2.3 years ago by
aindap110
United States
aindap110 wrote:

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?

ADD COMMENTlink modified 19 months ago by asur0 • written 2.3 years ago by aindap110
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gravatar for Petr Ponomarenko
2.3 years ago by
United States / Los Angeles / ALAPY.com
Petr Ponomarenko2.6k wrote:

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

ADD COMMENTlink written 2.3 years ago by Petr Ponomarenko2.6k
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gravatar for vmicrobio
2.3 years ago by
vmicrobio240
vmicrobio240 wrote:

I would use stampy or bowtie2 alignment tools

ADD COMMENTlink written 2.3 years ago by vmicrobio240
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gravatar for asur
19 months ago by
asur0
asur0 wrote:

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.

ADD COMMENTlink written 19 months ago by asur0
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