Bracken
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jenniferlu717
Kraken 2 + Bracken 2 Strain level?
Hello,
I wanted to ask for clarification. If I had my own database with strain sequences and their corresponding NCBI accession numbers, I assume Kraken 2 would be able to classify those reads at the strain level. I wanted to get clarification on whether Bracken 2 would also give abundance estimation at the strain level? Is this possible and if so, what other files or processes do I need to do this?
Thank you.
If there are unique kmers at the strain level, both Kraken 2 and Bracken should be able to work for your database. You will need to generate the databaseXmers.kmer_distrib file for the database after you build the Kraken database.
Hi Jennifer,
I had another question about this that I need clarification on. I had added in the taxids for subspecies in my nodes and names dmp files. All of my genome assembly files I used to build the Kraken2 library have the subspecies level taxids in their genome assembly headers so does this mean that my reads will be classified at subspecies level for Kraken2 + Bracken2?
If I had strain genome assemblies and wrote in their taxids in the headers instead, does this mean that reads will be classified at strain rank as the lowest level? I need clarification on how Kraken2 + Bracken2 classify at strain level. If I wrote subspecies in my nodes & names dmp files but those subspecies assemblies are actually at strain level, can I assume that the subspecies classifications will be strain rank (I'm not sure what the proper rank label for strain is in dmp files)?
Thank you.
I managed to build a strain level kraken db with flextaxd. Kraken2 worked fine but then bracken didn't worked. Do we have to change something in the code?
It had worked fine for me, but I might be forgetting some small change that I might've made when I ran Kraken & Bracken without error. What was the error that Bracken gave you?
@punnettsun sorry for the extremely late message, I think you opened this issue back up around when I was defending my thesis and I never got back around to answering. But yes, Kraken 2 and Bracken 2 can work with strain level classifications and abundance estimation. Kraken 2 will classify reads as specifically as possible and then Bracken 2 can readjust reads down to the subspecies level only if the subspecies level exists however. So if a species has no subspecies in the report file, those reads will be lost.
@SilasK bracken does work, but you need to specify level as S1 I believe for it to go below the species level. Is there an error message?
@jenniferlu717 Thank you, I was able to build a Kraken db at strain level and had Bracken work as well. Like you said, I had to make sure 'S1' was used.