James Ferguson

Install asking for python3 while using python 2

4

Hello, I am following on from this issue over at circtools ( https://github.com/dieterich-lab/circtools/issues/82 ) So I made a python2 venv, and while trying to install, it's now telling me I...

sometimes a run will crash or hit a wall limit due to hardware of system limits. It would be helpful to easily resume the sequencing run. I think a quick...

Progress shows a snapshot of chunked basecalled reads It would be good I it showed the full total at the ned as well 

Add some read-id list for selective basecalling

2

Allow a user to provide a list of read-ids to basecall. This will then use random access get calls to pyslow5

Add version checks for guppy and lib

2

After starting the guppy server but before connecting a client, I should do a check that the guppy server version matches the installed guppy client lib version. I think I...

Pyarrow error

10

Hey George, I have a user getting a strange error. I've attached the issue below, where you can also see some more context. Any ideas what the issue here might...

add barcoding info to the sequencing summary when turned on

1

Here is an example of the file format of a seq sum file when bacoding is turned on in minknow ``` filename_fastq filename_fast5 filename_pod5 parent_read_id read_id run_id channel mux minknow_events...

Add the tags here https://github.com/nanoporetech/dorado/blob/release-v0.7/documentation/SAM.md#sam-specification

Add model version to output

3

When ` --config dna_r10.4.1_e8.2_400bps_5khz_modbases_5mc_sup_prom.cfg` is given as the model, this doesn't say what the model version is for matching with clair3 variant calling models. To fix this, I should pull...

Enable duplex calling with the fake 10 read hack to force the basecaller to spit the called reads for a channel out. It looks like v7.4.12 dorado server has not...