Hi,
I am trying to map metagenomic data to a set of more than a thousand genomes.
I expect many of the reads not to align to anything as it is metagenomic data and there are many bugs out there that do not have a reference genome.
I am not sure what would be the best alignment tool in this case. Was thinking about Bowtie2 but as far as I understand I will need to index each of the reference genomes separately and run each of my samples against each of the indexes.
Any suggestions?
Thanks,
Marie
I am trying to map metagenomic data to a set of more than a thousand genomes.
I expect many of the reads not to align to anything as it is metagenomic data and there are many bugs out there that do not have a reference genome.
I am not sure what would be the best alignment tool in this case. Was thinking about Bowtie2 but as far as I understand I will need to index each of the reference genomes separately and run each of my samples against each of the indexes.
Any suggestions?
Thanks,
Marie
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