Host sequences filtering

[lusine Khachatryan]

Hello! 

I wonder whether this pipeline removes somehow possible host contaminations?

Regards,

Lusine Khachatryan

[Sam Westreich]

Hi Lusine,

No, there is not a built-in step for host contamination removal, but doing so is fairly straightforward.  If you know your host genome, you could simply run a tool like BWA-MEM, ideally after step 3 (ribodepletion) and before step 4 (annotation against the DIAMOND database).  You could add it to the master script at line 222: https://github.com/transcript/samsa2/blob/master/bash_scripts/master_script.sh

You'd simply get your reference genome and use the bwa mem command to align your sequence fastq against that reference.

With BWA-MEM, you'd get a BAM file that contains both mapped and unmapped reads.  You could then use SAMtools to extract the unmapped reads from the BAM, with a command like:

samtools view -f 4 file.bam > unmapped.sam

You'd then simply convert this sam file back into a fastq (this can be done with Unix command line commands), and then continue on with the rest of the SAMSA2 pipeline as normal.

Best,

Sam

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Sam Westreich, PMP, PhD

Microbiome Scientist, DNAnexus, 

http://www.mosaicbiome.com

[lusine Khachatryan]

Dear Sam,

Thank you! Yes, what you've described (mapping on human genome after the ribodepletion) is basically what I've done. But I did not get any host contaminations and therefore I thought there is a "hidden" filtering somewhere in your pipeline. Thank you one more time for the explanation.

Regards,

Lusine