Question: Assembly pipeline De Novo | Reference
1
gravatar for elbecerrasoto
3.9 years ago by
United States
elbecerrasoto30 wrote:

I have SRA IDs to download Salmonella sequences from the SRA NCBI web page. Then I need to assemble it. It is a valid a approach to do a De Novo assembly and then a  Reference assembly with the output contigs/scaffolds of De Novo asembly. For example doing first a De Novo assembly with SPAdes and then mapping with BWA to my reference. My goal is to get a good assembly and then perform an annotation and in the end do a pangenomic analysis of the genomes. I am interested principally in the Newport serovar, so I am not sure if only doing the reference assembly with the genome of Salmonella enterica Typhimurium from NCBI or if in the end will be better to do De Novo assembly and the improve it with the reference.

assembly • 1.8k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by elbecerrasoto30

Check here.

However, what is your goal? For Salmonella, there are several finished genomes, why not choose one of those as reference?

ADD REPLYlink written 3.9 years ago by h.mon27k

My goal is to get a good assembly and then perform an annotation and in the end do a pangenomic analysis of the genomes. I am interested principally in the Newport serovar, so I am not sure if only doing the reference assembly with the genome of Salmonella enterica Typhimurium from NCBI or if in the end will be better to do De Novo assembly and the improve it with the reference.

ADD REPLYlink written 3.9 years ago by elbecerrasoto30
1
gravatar for Antonio R. Franco
3.9 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.1k wrote:

If you can get a trusted Salmonella genome, I recommend you to use an assembler (such as Velvet, etc..) and then do a comparison between your assembly and the trusted genome with a program like Mauve

You will need to check how well the assembler work after selecting several k-mer for the assembling, since the choice of this kmer influences a lot the assembly itself

In the absence of a trusted genome to compare, chances to get a weird draft genome is high. 

ADD COMMENTlink written 3.9 years ago by Antonio R. Franco4.1k
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