Question: Host Decontamination: bbTools or Samtools?
0
gravatar for lotus28
10 months ago by
lotus2870
lotus2870 wrote:

Hi,

I have always used Samtools to remove any human contaminants from my gut flora data. However, bbTools also allows you to do that. All the post I've seen mention using bbTools for small contaminants removal. Is it practical to use it for removing hg19 contaminants or should I stick with Bowtie + Samtools?

ADD COMMENTlink modified 10 months ago by genomax84k • written 10 months ago by lotus2870

I have always used Samtools to remove any human contaminants from my gut flora data.

Well, samtools has multiple subcommands, and you can do a lot with it. It is probably most helpful if you describe more in detail what you did (which commands you used).

ADD REPLYlink written 10 months ago by WouterDeCoster43k

Basic samtools stuff: align against hg19 with bowtie2, extract reads with both ends unmatched, sort and convert filtered bams to fastq.

I was just wondering if I could remove one docker container from my pipeline by using bbTools for both quality trimming and decontamination

ADD REPLYlink written 10 months ago by lotus2870

Yes you can do that.

ADD REPLYlink written 10 months ago by genomax84k
3
gravatar for genomax
10 months ago by
genomax84k
United States
genomax84k wrote:

Yes it is totally practical. @Brian Bushnell wrote a pipeline (which uses BBTools) to do that. You can find the post here. You could also use bbsplit.sh from BBMap tools and bin your reads in multiple ways.

ADD COMMENTlink modified 10 months ago • written 10 months ago by genomax84k

Yesterday I ran some tests to compare bowtie2 and bbTools decontamination. I used the same index provided in your link for both. bbTools takes longer to compute (15-30% longer) and deletes fewer reads. It also seems like bbTools has lower sensitivity, even in heavily contaminated runs. I think I will stick with my previous workflow.

ADD REPLYlink modified 10 months ago • written 10 months ago by lotus2870

I assume you tried the default options for everything. While you can stay with your pipeline I am sure there are options with bbtools that one can tweak to get results as good as what ever you are doing currently.

ADD REPLYlink written 10 months ago by genomax84k

Yes, probably tweaking bbTools pipeline might work, but I have not noticed any significant gain in speed to justify this tweaking. For the time being I will just stick with my current pipeline.

ADD REPLYlink written 10 months ago by lotus2870
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