Question: mapping unmapped reads to viral genome using blast+
0
gravatar for Shaway
11 weeks ago by
Shaway10
Shaway10 wrote:

Hello everyone,

I encountered small questions when analyzing AD patients' blood DNA NGS data. After mapping sequencing data to hg19 genome, I want mapping the remaining unmapped reads to viral genome. I found viral genome reference on ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/, but there are 3 files (viral.1.1.genomic.fna.gz, viral.2.1.genomic.fna.gz, viral.3.1.genomic.fna.gz).

I merged these 3 files and using blast to mapping unmapped reads to the reference. Is it right?

The mapping is so slow(20 cores dealing with 20000000 reads). Does anyone knows any methods to do this faster?

Thanks!!!

balst blastn virus alignment ngs • 254 views
ADD COMMENTlink modified 10 weeks ago by Philipp Bayer6.0k • written 11 weeks ago by Shaway10
3

Blast is not the right tool for doing this. You should switch back to an NGS data aligner.

ADD REPLYlink written 11 weeks ago by genomax63k
2
gravatar for Philipp Bayer
10 weeks ago by
Philipp Bayer6.0k
Australia/Perth/UWA
Philipp Bayer6.0k wrote:

Looks like you're looking for a metagenomics tool - tools like Kraken 2 or Centrifuge are much faster for what you want to do

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Philipp Bayer6.0k

Do you have a preference on one tool over another?

ADD REPLYlink written 10 weeks ago by Gjain5.3k

Not really, no - Kraken2 is so new that I haven't seen any benchmarks yet. Kraken1 was slower but more accurate (IIRC)

ADD REPLYlink written 10 weeks ago by Philipp Bayer6.0k

Thanks for the information ...I will try Kraken2

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Gjain5.3k

Thank you very much! I will try these 2 tools.

ADD REPLYlink written 10 weeks ago by Shaway10
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