Hi all,
I’m currently processing metagenomic/virome data and want to remove potential host contamination. I have multiple host genomes (e.g., human, sheep) that I want to use as references for host filtering with BWA.
My question is: is it acceptable to concatenate all host genomes into a single large FASTA file, build a single BWA index, and then map reads to this combined reference to remove host reads?
I’m mainly concerned about whether this approach might introduce any biases or mapping errors compared to building separate indices for each host genome. I’m not worried about missing reads (false negatives), but I want to avoid incorrectly removing reads (false positives).
Has anyone tried this approach in practice? Are there any known caveats or recommended alternatives?
Thanks in advance for your advice!
1 answer
It should be fine to build a single multi-fasta file. Alignment program does not know or care that you have more than one genome in there and sounds like you don't either (you just want to remove the reads).
That said, you can also look into bbsplit from BBMap suite that can allow you to intelligently manage read assignments to single/multiple genomes in case you were also interested in finding out which reads map to which genome: https://bbmap.org/tools/bbsplit
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You can check the following benchmark paper, which describes the strengths and weaknesses of the most commonly used host contamination removal methods.
https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf004/8045180