Best software to get summary statistics from nanopore sequencing runs
Hi,
I'm looking for the recommended software to get summary statistics for nanopore sequencing experiments. I'm currently using Mosdepth to estimate coverage and depth across different sequencing runs, but I'm looking for a program that will give me more info.
Specifically I'm looking for a program that will tell me the mean, median, and mode read lengths, the minimum read length, the maximum read length, and the N50.
I came across nanostat (https://github.com/wdecoster/nanostat) but I'm wondering if there are better/other recommended softwares.
1 answer
You want cramino which is a replacement for nanostat.: Introducing Cramino: a *fast* QC tool for long reads
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Have you looked at pycoQC?
PycoQC is great but it requires the original sequencing summary file from the run to work.