Getting species counts from Illumina metagenome data
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5.9 years ago
lotus28 ▴ 70

I want to use SparCC for correlation analysis on metagenome samples but it requires raw counts as it has a special way of estimating community composition.

I am completely new to this field and have no idea of what programs can give me raw counts.
Could you suggest a program that does that from Illumina WGS?

So far I have considered Metaphla2 the best option.
But is there a way to make Metaphlan2 output species counts instead of relative abundances?

In its help I have found the options concerning count normalization but I'm not sure they will produce the result I need.

metagenome species composition wgs metaphlan2 • 1.7k views
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Kraken may also be useful.

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