0
$\begingroup$

Hope all of you are fine. I am wondering if exists a program easy to use that can bring me Basic Statistics of Quality Control from raw data made by MinION device (nanopore).

I have read about FASTAQC and Porechop. My sequencing raw data was a result of a metagenomics analysis (16s and 18s). My main objective is only to filter the sequences and obtain a basic statistic about the lenght and the number of sequences ordered by the lenght. Thank you ladies and gentlemen

PD Sorry for my poor english. Day to day i'm trying to improve it.

$\endgroup$
1
$\begingroup$

A simple start would be to use MinIONQC, which is also available via bioconda under the name r-minionqc.

$\endgroup$
1
$\begingroup$

I assume raw data is in Fastq format, but ideally you should also use the sequencing_summary.txt file generated by the basecaller. Other alternatives for QC are PycoQC and NanoPlot. I developed and maintain NanoPlot, so let me know if there is something I can help you with.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.