Tweet
Does anyone know of a tool to convert fast5 data to fastq?
-
-
I do not understand the the fast5/hdf format very well. Most likely such a converter is not universal? Here is one:
This certainly needs to be amended if the data are located in other "directories" of the fast5 file when using a different pipeline.Last edited by luc; 06-20-2014, 08:45 AM. -
Sorry, the mentioned script generates FASTAs. But upon replacing "fasta" with "fastq" in line 17 it will generate indeed FASTQ files.
Originally posted by luc View PostComment
-
There's a five line python script in the Metrichor docs that shows you how to do this.Comment
-
Yes, but these 5 lines are not a complete script and they do not seem to work very well - this might be a problem on my side?.Originally posted by Bukowski View Post
Nick's script has some advantages there.Comment
-
I had problems installing the hdf5 python libraries, so resorted to PDL::IO::HDF5 and Perl.Originally posted by luc View PostComment
-
I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...Yesterday, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment