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Hello,
I will be doing metagenomic sequencing on clinical samples with >99% expected human reads and few microbial reads, with the microbial reads being of interest.
There will be no assembly (way too low bacterial coverage), and thus each read should be classified against the refseq database of bacteria, virus, fungi, and the human genome.
Which tools would you suggest to use for this task? I have considered kraken2 and bowtie2. Computational power is not a limitation
Morten
I will be doing metagenomic sequencing on clinical samples with >99% expected human reads and few microbial reads, with the microbial reads being of interest.
There will be no assembly (way too low bacterial coverage), and thus each read should be classified against the refseq database of bacteria, virus, fungi, and the human genome.
Which tools would you suggest to use for this task? I have considered kraken2 and bowtie2. Computational power is not a limitation
Morten