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Issue12/add_barcoding_kits_and_sample_rate #13

Merged
merged 21 commits into from
Jul 10, 2024
Merged

Issue12/add_barcoding_kits_and_sample_rate #13

merged 21 commits into from
Jul 10, 2024

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Adoni5
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@Adoni5 Adoni5 commented Apr 29, 2024 •
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Adds one new MinKNOW API endpoint - get_sample_rate and adds the meta_info field to get_run_info, which contains the information readfish needs to accept barcoding kits.

Also changes the level of one very noisy debug log to debug from info

The added barcoding kits are:

  1. EXP-NBD114
  2. EXP-NBD103
  3. EXP-NBD104
  4. EXP-PBC01
  5. EXP-PBC096

This should allow guppy or dorado to demultiplex barcodes in the latest readfish versions now.

Added get_sample_rate for upcoming readfish versions, and the sample rate is taken from the simulation profile toml, under the parameters section.

Adoni5 and others added 20 commits April 29, 2024 10:31
@Adoni5
Add the end point for the available barcoding kits in protocol proto
a7441ca
@Adoni5
Add sample rate endpoint for readfish >= 2024.X.X
6aef351
@Adoni5
Change debug logs to debug! from info!
42d0280
@Adoni5
Update R9 example profiles
962af7e
@Adoni5
Update R10 barcoded toml
f30b997
@Adoni5
Add noise to R10 squiggle to vastly improve performance
9423c1c
@Adoni5
Don't add digitisation. I have no idea what effect this has on downst…
0998001 
…ream basecalling, but it makes readfish base-calling a lot better
@Adoni5
Set the conencted guppy version to 7.3.9. WILL LIMIT readfish compati…
db9d503 
…bility to 2024.2.0
@satriobio
Revert "Add noise to R10 squiggle to vastly improve performance"
e772827 
This reverts commit 9423c1c.
@satriobio
barcode is now R10, 5kHZ with a newly derived model works well
9ac641e
@satriobio
Include digitisation, range, scale and offset on sim.
8f46f13 
Send them over the device RPC, so readfish uses the correct values when base calling.
@satriobio
Update prefix squiggle
a5d10c9
@satriobio
newly derived model for R10 5Khz, using MEAN 100.5 and Std dev 23.5
1f39738
@satriobio
Mutate the signal vec in place for ADC values
5d87550
@satriobio
Fix clippy warnings
17c499e
@satriobio
Add rayon
7311d86
@satriobio
Add Laplace noise in first iteration of R10 signal
ffd2461 
parallelise conversion to ADC
@Adoni5
Implement the experiment_duration flag to actually work, needs docs u…
9eb22bf 
…pdating
@Adoni5
5Khz human barcoded toml
cf27f12
@Adoni5
Set PoreType to NotSet for POD5 output
2567e9b 
Upgrades Podders to 0.1.4, which has the NotSet PoreType Enum variant.
This matches MinKNOW which also doesn't set this field.
@Adoni5
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Adoni5 commented Jul 10, 2024

Okay this should provide better R10 barcode signal, and provides more realistic values in the POD5 files for basecalling.
Sets the PoreType for POD5 output as not-set, which is apparently what MinKNOW sets it as.
Also does everything listed above -

Adds one new MinKNOW API endpoint - get_sample_rate and adds the meta_info field to get_run_info, which contains the information readfish needs to accept barcoding kits.

Also changes the level of one very noisy debug log to debug from info

The added barcoding kits are:

EXP-NBD114
EXP-NBD103
EXP-NBD104
EXP-PBC01
EXP-PBC096

This should allow guppy or dorado to demultiplex barcodes in the latest readfish versions now.

Added get_sample_rate for upcoming readfish versions, and the sample rate is taken from the simulation profile toml, under the parameters section.

@Adoni5 Adoni5 merged commit 3c62096 into main Jul 10, 2024
@Adoni5 Adoni5 mentioned this pull request Jul 11, 2024
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@Adoni5 @satriobio