PathoTracker huilab

PathoTracker

Software version: 1.0.0 (2023-03)
Database version: (2022-07-28)

Example sequence format

We recommend filling in the correct email address,
the software will take some time to run, we will send the result file to your email.

If you don’t want to provid your email, please stay on the waiting page or make a note of the sample name on the waiting page. You can visit the result interface after a certain period of time to retrieve the results.
The page can access as follows:
http://pathotracker.pku.edu.cn/waiting_page/your_sample_name/
http://pathotracker.pku.edu.cn/result/your_sample_name/
Check the example input (Clinical Metagenomic Nanopore sequencing data)
Check the example output

We recommend you obtain the Klebsiella pneumoniae sequence from the "filename-result.tsv" in the "species detection" result, extract the Klebsiella pneumoniae sequence using the following command, compose the fasta and submit it to this page for Attribute determination.

seqtk subseq filename.fq.gz filename-kpn-list-nouniq.txt >filename-kpn-nouniq.fq
seqtk seq -A filename-kpn-nouniq.fq > filename.fasta

Select database :

Select threshold for minimum % identity (virulence genes) :

Select threshold for minimum % identity (antimicrobial genes) :

Select minimum % coverage (virulence genes) :

Select minimum % coverage (antimicrobial genes) :

Whether to join us : (We will not save your data if you don't click this checkbox)

I confirm that I have read and understood the disclaimer before uploading any data

Select your country : (No need to fill in if you don't want to save your data)

Email (Not mandatory)

Select type of your sequence :

Select type of your sample :
Third generation sequencing(TGS)
Next-generation sequencing(NGS)

Choose file:

Components

PathoTracker