update dev from main

README.md

@@ -17,13 +17,6 @@ You can download guppy or dorado server here: https://community.nanoporetech.com
 - Currently, the main branch is the multi-process version (parallel processes to communicate to/from Guppy client) that enables performance scaling for multi-GPU setups, especially for FAST basecalling or shorter reads. A simple single-process version (one process to communicate to/from the Guppy client) that works well for HAC and SUP models is available in the `singleproc` branch for learning purposes. 
 - Before v0.3.3, the main branch was the single-process version (`singleproc` branch) and the multi=process version was under the `multiproc` branch.
 
-## Dorado basecalls not matching
-
-Currently if you basecall the same data with `dorado==0.3.4`, `dorado_basecall_server`/`ont_basecall_client==7.4.1`, and `ont-pyguppy-client-lib==7.4.1`, you will get 3 different answers.
-We are following up with ONT why this is the case. The output is very close, but not identical in the base calls.
-
-There is no such issue with the latest guppy build, `6.5.7`.
-
 
 # Quickstart
 

docs/param.md

@@ -1,10 +1,22 @@
-The mysterious default parameters in Guppy.
-
-- Guppy 4.0.11 [dna_r9.4.1_450bps_hac_prom] (qscore cut off default:7)
-- Guppy 6.4.2 [dna_r9.4.1_450bps_fast_prom] (qscore cut off - default:8)
-- Guppy 6.4.2 [dna_r9.4.1_450bps_hac_prom] (qscore cut off - default:9)
-- Guppy 6.4.2 [dna_r9.4.1_450bps_sup_prom] (qscore cut off - default:10)
-- Guppy 6.4.2 [dna_r10.4.1_e8.2_400bps_fast_prom] (qscore cut off - default 8) 
-- Guppy 6.4.2 [dna_r10.4.1_e8.2_400bps_hac_prom] (qscore cut off - default 9)
-- Guppy 6.4.2 [dna_r10.4.1_e8.2_400bps_sup] (qscore cut off - default 10)
+# The mysterious default parameters in Guppy
+
+##  qscore cutoff 
+
+The qscore cutoff (that determine pass/fail) in Guppy keeps on changing and there is no easy way to get this. So this is an attempt to document based on what we find.
+
+
+| Guppy version | Model                         | default qscore cut off |
+|--------       |------                         | ---                    | 
+| 6.5.7         | dna_r10.4.1_e8.2_400bps_5khz_hac_prom   |      9                   |
+| 6.5.7         | dna_r10.4.1_e8.2_400bps_5khz_sup   |      10                   |
+|               |                               |                      | 
+| 6.4.2         | dna_r9.4.1_450bps_fast_prom   |    8                   |
+| 6.4.2         | dna_r9.4.1_450bps_hac_prom    |    9                   |
+| 6.4.2         | dna_r9.4.1_450bps_sup_prom    |    10                  |
+| 6.4.2         | dna_r10.4.1_e8.2_400bps_fast_prom   |      8                   |
+| 6.4.2         | dna_r10.4.1_e8.2_400bps_hac_prom   |      9                   |
+| 6.4.2         | dna_r10.4.1_e8.2_400bps_sup   |      10                  |
+|               |                               |                      | 
+| 4.0.11        | dna_r9.4.1_450bps_hac_prom    | 7                      |
+
 

src/_version.py

@@ -1 +1 @@
-__version__="0.4.0"
+__version__="0.4.1"