Question: Best Practice To Find Human Contamination In Microbiome?
3
gravatar for Iddo
7.7 years ago by
Iddo230
Iddo230 wrote:

I have gut human microbiome data, I would like to filter out human sequences. What would be the best practice? I thought of megablasting the reads (454) against the human genome and removing 100% identities. Any ideas to make this better / shorter?

Thanks,

Iddo

metagenomics human • 1.7k views
ADD COMMENTlink written 7.7 years ago by Iddo230
5
gravatar for lh3
7.7 years ago by
lh331k
United States
lh331k wrote:

BWA-SW if you really care about speed. Or ssaha2 or blat if you are more comfortable with traditional tools.

ADD COMMENTlink written 7.7 years ago by lh331k
1
gravatar for Casey Bergman
7.7 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

If you have shotgun metagenomic data, this sounds like a reasonable plan - though you could swap out megabalst for a different/faster aligner like BLAT, and allow some degree of mismatch for sequencing error. If you have have targeted metagenomic data (e.g. a 16S amplicon), then you could additionally impose a filter for contamination hits to be off-target (e.g. non-16S).

ADD COMMENTlink written 7.7 years ago by Casey Bergman18k
0
gravatar for Wolfgang
7.7 years ago by
Wolfgang0
Wolfgang0 wrote:

If BLASTN against the NCBI-NT is possible for the reads, you could also try to use CARMA3 to filter out human sequences...

ADD COMMENTlink written 7.7 years ago by Wolfgang0
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