Hasindu Gamaarachchi
@hasindu2008.bsky.social
Lecturer at UNSW Sydney; Visiting Scientist at Garvan Institute of Medical Research -
Designing embedded systems for bioinformatics applications.
Designing embedded systems for bioinformatics applications.
possibly because ONT use their POD5 format which is not great on HDD. They could have adopted our slow5 format which we showed long ago that works for even HDD, before pod5 came in.
Now the pod5 (while indeed better than fast5) is still behind slow5 in this regards
academic.oup.com/gigascience/...
Now the pod5 (while indeed better than fast5) is still behind slow5 in this regards
academic.oup.com/gigascience/...
The enduring advantages of the SLOW5 file format for raw nanopore sequencing data
Abstract. Nanopore sequencing is a widespread and important method in genomics science. The raw electrical current signal data from a typical nanopore sequ
academic.oup.com
October 30, 2025 at 5:01 AM
possibly because ONT use their POD5 format which is not great on HDD. They could have adopted our slow5 format which we showed long ago that works for even HDD, before pod5 came in.
Now the pod5 (while indeed better than fast5) is still behind slow5 in this regards
academic.oup.com/gigascience/...
Now the pod5 (while indeed better than fast5) is still behind slow5 in this regards
academic.oup.com/gigascience/...
Sometime ago I changed a configuration file so this location is changed to our /data location permanently. Don't know if they have changed this option now.
October 30, 2025 at 4:55 AM
Sometime ago I changed a configuration file so this location is changed to our /data location permanently. Don't know if they have changed this option now.
Yeh, many better ways exist. We just showed how the most naive method can still keep up truck load volumes of data.
October 21, 2025 at 4:05 AM
Yeh, many better ways exist. We just showed how the most naive method can still keep up truck load volumes of data.
In my personal opinion, more popular it is, more care should be taken to avoid compatibility problems. Adhoc implementation-driven changes can be avoided if enough thought is given at the design phase.
October 21, 2025 at 4:04 AM
In my personal opinion, more popular it is, more care should be taken to avoid compatibility problems. Adhoc implementation-driven changes can be avoided if enough thought is given at the design phase.
Just checked my logs and yes it is true.
The output produced was wrong - A simple program that sums up the signal values.
I just checked release logs of pod5 - 0.0.20 "Fix bug reading data via C API". So it could be a bug that got introduced in before.
The output produced was wrong - A simple program that sums up the signal values.
I just checked release logs of pod5 - 0.0.20 "Fix bug reading data via C API". So it could be a bug that got introduced in before.
October 21, 2025 at 4:04 AM
Just checked my logs and yes it is true.
The output produced was wrong - A simple program that sums up the signal values.
I just checked release logs of pod5 - 0.0.20 "Fix bug reading data via C API". So it could be a bug that got introduced in before.
The output produced was wrong - A simple program that sums up the signal values.
I just checked release logs of pod5 - 0.0.20 "Fix bug reading data via C API". So it could be a bug that got introduced in before.
October 16, 2025 at 10:21 PM
Meanwhile, questions by me and @psy-fer.bsky.social on POD5 writing opened months ago are yet to be answered by ONT.
It is very interesting that they have skipped those questions 🤣
It is very interesting that they have skipped those questions 🤣
September 12, 2025 at 12:45 PM
Meanwhile, questions by me and @psy-fer.bsky.social on POD5 writing opened months ago are yet to be answered by ONT.
It is very interesting that they have skipped those questions 🤣
It is very interesting that they have skipped those questions 🤣
Any possibility of getting something akin to the "lowQ.bed" that hifiasm output indicating the low-quality regions in the assembly?
September 12, 2025 at 8:09 AM
Any possibility of getting something akin to the "lowQ.bed" that hifiasm output indicating the low-quality regions in the assembly?
Nice!
We plan to try this out with adaptive sampling for metagenomes, like we did in cornetto with hifiasm [https://doi.org/10.1101/2025.03.31.646505] for genome assemblies.
We plan to try this out with adaptive sampling for metagenomes, like we did in cornetto with hifiasm [https://doi.org/10.1101/2025.03.31.646505] for genome assemblies.
September 11, 2025 at 6:31 AM
Nice!
We plan to try this out with adaptive sampling for metagenomes, like we did in cornetto with hifiasm [https://doi.org/10.1101/2025.03.31.646505] for genome assemblies.
We plan to try this out with adaptive sampling for metagenomes, like we did in cornetto with hifiasm [https://doi.org/10.1101/2025.03.31.646505] for genome assemblies.
seriously?
I am glad that some time ago, I disabled this Gemini summary from my search results when it was pushed out. Seems I should better keep it that way😂
I am glad that some time ago, I disabled this Gemini summary from my search results when it was pushed out. Seems I should better keep it that way😂
September 9, 2025 at 3:05 PM
seriously?
I am glad that some time ago, I disabled this Gemini summary from my search results when it was pushed out. Seems I should better keep it that way😂
I am glad that some time ago, I disabled this Gemini summary from my search results when it was pushed out. Seems I should better keep it that way😂
July 21, 2025 at 9:05 AM
For reference based frequency finding, thought taking the bases that only match the ref could be a better choice. But yes, such a warning is indeed something that would be valuable.
Thank you very much for the suggestion
Thank you very much for the suggestion
July 18, 2025 at 11:43 AM
For reference based frequency finding, thought taking the bases that only match the ref could be a better choice. But yes, such a warning is indeed something that would be valuable.
Thank you very much for the suggestion
Thank you very much for the suggestion
I get these then,
6754
6751
6769
6760
6756
Which seem to match the expected, assuming you are using 1-based coordinates
6754
6751
6769
6760
6756
Which seem to match the expected, assuming you are using 1-based coordinates
July 18, 2025 at 6:44 AM
I get these then,
6754
6751
6769
6760
6756
Which seem to match the expected, assuming you are using 1-based coordinates
6754
6751
6769
6760
6756
Which seem to match the expected, assuming you are using 1-based coordinates
pass the option --insertions, so that the CIGAR is parsed for inserted bases
July 18, 2025 at 5:50 AM
pass the option --insertions, so that the CIGAR is parsed for inserted bases