What is the input file for kraken to create krona plots?

Question

[arunsaikirans]

Hey guys,

I am trying to create krona plots for metagenomic data,for that the output from kraken is used.I have now installed kraken and krona.But I have no idea how to start working. PLS tell me about the databases and minikraken.I have heard that minikraken is sufficient. Could someone help me with the commands I have tried searching but its not clear for me,need help with the commands..

Kiran

[cschu181]

Can you tell us where you have tried searching? The official documentation at https://ccb.jhu.edu/software/kraken/MANUAL.html is quite well written and provides everything that you need to get started with kraken.

Answer 1

[Sej Modha]

Kraken is a k-mer based taxonomic classification tool that can classify input sequences using k-mers (short sequences usually of length 31) from input datafiles (e.g. fasta or fastq). Taken from Kraken website

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.

Kraken requires a database of short sequences for classification, please refer to the Kraken webpage for further details, also refer to the paper: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46

KronaTools(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-385) can be used to visualised the taxonomy classification generated using Kraken.