Hi, I carried out a NGS analysis(resequencing).
I got variant calling data and raw data(fastq).
I convert fastq file to fasta file and opened with text reader program.
What I found was about tens of millions of seqeunce fragments.
Is it possible to assemble resequencing fragments to whole genome sequence? I want a result like de novo sequencing.
Thank you
Hi,
if you want to perform a denovo assembly, after cleaning your reads, you can use the good-quality reads to perform the assembly. You can use SPAdes (http://bioinf.spbau.ru/spades). It's very easy to use and you'll obtain you genome assembled. The only limitation of SPAdes is the amount of RAM your computer can use to perform the analysis. Actually is one of the best assembler for denovo purpose.
If you want to use other tools such SOAPdenovo, ALLPATHS, etc, then you could compare their results using QUAST (Article QUAST: Quality assessment tool for genome assemblies
).If you want to perform a reference guided assembly, you can contact https://www.sequentiabiotech.com/; them developed a tool (Reconstructor, https://www.sequentiabiotech.com/omicstools/pipeline/ , Article Careful with That Axe, Gene, Genome Perturbation after a PEG...
) for such situation.Best regards,
Domenico
Thank you so much for your kind reply. I've talked to a company that has run NGS and I've heard that reads analyzed by Hiseq have much poor quality than pacbio, so now I'm thinking about what to do.
I knew that there would be so many reads. At first, I did NGS analysis just for variant calling but I became interested in additional analysis. That's why I asked this question.
Thank you again.
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