Can we get fastq read id of certain species that kraken assigned?

Question

[grkorompis]

So after finished running the kraken, we get a table of abundance list as one of the output. After seeing the top 10, my species of interest seem to land on 8th spot, with not much of reads compared to the top 3, it was 17 reads in total. I wanted to to check the length and sequence of this read, so my questions are:

1. Can we get read id so that I could extract those id from the input fastq files, or can we directly get the sequence and its lenghts from kraken for those 17 reads in my species of interest?
2. How many reads are enough to trust kraken assignment result?

Thank you.

Answer 1

[MatthewP]

Hey, you can get reads id from kraken2 output, check kraken2 output format