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update profiles to latest guppy 6.5.7
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@hiruna72
hiruna72 committed Feb 5, 2024
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36 changes: 26 additions & 10 deletions docs/move_table.md
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Expand Up @@ -24,16 +24,32 @@ The second move corresponds with `2 x stride` signal points. The third with `4 x

Different models have different strides. Strides from some of the guppy models are listed below.

| Model | Stride |
|----------------------------------|--------|
| dna_r10.4.1_e8.2_400bps_fast.cfg | 5 |
| dna_r10.4.1_e8.2_400bps_hac.cfg | 5 |
| dna_r10.4.1_e8.2_400bps_sup.cfg | 5 |
| dna_r9.4.1_450bps_fast_prom.cfg | 5 |
| dna_r9.4.1_450bps_hac_prom.cfg | 5 |
| dna_r9.4.1_450bps_sup_prom.cfg | 5 |
| rna_r9.4.1_70bps_hac_prom.cfg | 10 |
| rna_r9.4.1_70bps_fast_prom.cfg | 12 |
| Model | Stride | Guppy version |
|---------------------------------------|--------|---------------|
| dna_r10.4.1_e8.2_400bps_fast.cfg | 5 | v6.3.7 |
| dna_r10.4.1_e8.2_400bps_hac.cfg | 5 | v6.3.7 |
| dna_r10.4.1_e8.2_400bps_sup.cfg | 5 | v6.3.7 |
| dna_r9.4.1_450bps_fast_prom.cfg | 5 | v6.3.7 |
| dna_r9.4.1_450bps_hac_prom.cfg | 5 | v6.3.7 |
| dna_r9.4.1_450bps_sup_prom.cfg | 5 | v6.3.7 |
| rna_r9.4.1_70bps_fast_prom.cfg | 12 | v6.3.7 |
| rna_r9.4.1_70bps_hac_prom.cfg | 10 | v6.3.7 |
| | | |
| dna_r10.4.1_e8.2_400bps_fast.cfg | 5 | v6.5.7 |
| dna_r10.4.1_e8.2_400bps_fast_prom.cfg | 5 | v6.5.7 |
| dna_r10.4.1_e8.2_400bps_hac.cfg | 5 | v6.5.7 |
| dna_r10.4.1_e8.2_400bps_hac_prom.cfg | 5 | v6.5.7 |
| dna_r10.4.1_e8.2_400bps_sup.cfg | 5 | v6.5.7 |
| dna_r9.4.1_450bps_fast.cfg | 5 | v6.5.7 |
| dna_r9.4.1_450bps_fast_prom.cfg | 5 | v6.5.7 |
| dna_r9.4.1_450bps_hac.cfg | 5 | v6.5.7 |
| dna_r9.4.1_450bps_hac_prom.cfg | 5 | v6.5.7 |
| dna_r9.4.1_450bps_sup.cfg | 5 | v6.5.7 |
| dna_r9.4.1_450bps_sup_prom.cfg | 5 | v6.5.7 |
| rna_r9.4.1_70bps_fast_prom.cfg | 12 | v6.5.7 |
| rna_r9.4.1_70bps_fast.cfg | 12 | v6.5.7 |
| rna_r9.4.1_70bps_hac.cfg | 10 | v6.5.7 |
| rna_r9.4.1_70bps_hac_prom.cfg | 10 | v6.5.7 |

As of [dorado_v0.4.0](https://github.com/nanoporetech/dorado/tree/v0.4.0) stride is used in three stages.
1. In the process of creating chunks to feed into the NN model ([code](https://github.com/nanoporetech/dorado/blob/b2af8e828a03d85448bb39ee5629660e6ef5e74f/dorado/read_pipeline/BasecallerNode.cpp#L78)).
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40 changes: 29 additions & 11 deletions docs/profiles.md
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Expand Up @@ -6,17 +6,35 @@ This document lists the different profiles.
The following precomputed kmer length and signal move offset values are available as profiles.
These profiles are used in `reform` tool. More information can be found at [reform](reform.md) and [calculate_offsets](calculate_offsets.md).

| | basecaller version | profile name | kmer length | sig move offset |
|-----|--------------------|------------------------------------|-------------|-----------------|
| DNA | guppy_v6.3.7 | guppy_dna_r9.4.1_450bps_fast_prom | 3 | 2 |
| DNA | guppy_v6.3.7 | guppy_dna_r9.4.1_450bps_hac_prom | 3 | 2 |
| DNA | guppy_v6.3.7 | guppy_dna_r9.4.1_450bps_sup_prom | 4 | 3 |
| DNA | guppy_v6.3.7 | guppy_dna_r10.4.1_e8.2_400bps_fast | 1 | 0 |
| DNA | guppy_v6.3.7 | guppy_dna_r10.4.1_e8.2_400bps_hac | 1 | 0 |
| DNA | guppy_v6.3.7 | guppy_dna_r10.4.1_e8.2_400bps_sup | 1 | 0 |
| | | | | |
| RNA | guppy_v6.3.7 | guppy_rna_r9.4.1_70bps_fast_prom | 1 | 0 |
| RNA | guppy_v6.3.7 | guppy_rna_r9.4.1_70bps_hac_prom | 1 | 0 |
| | basecaller versions | profile name | kmer length | sig move offset |
|---------|---------------------|-----------------------------------------|-------------|-----------------|
| ~~DNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_dna_r9.4.1_450bps_fast_prom~~ | ~~3~~ | ~~2~~ |
| ~~DNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_dna_r9.4.1_450bps_hac_prom~~ | ~~3~~ | ~~2~~ |
| ~~DNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_dna_r9.4.1_450bps_sup_prom~~ | ~~4~~ | ~~3~~ |
| ~~DNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_dna_r10.4.1_e8.2_400bps_fast~~ | ~~1~~ | ~~0~~ |
| ~~DNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_dna_r10.4.1_e8.2_400bps_hac~~ | ~~1~~ | ~~0~~ |
| ~~DNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_dna_r10.4.1_e8.2_400bps_sup~~ | ~~1~~ | ~~0~~ |
| | | | | |
| ~~RNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_rna_r9.4.1_70bps_fast_prom~~ | ~~1~~ | ~~0~~ |
| ~~RNA~~ | ~~guppy_v6.3.7~~ | ~~guppy_rna_r9.4.1_70bps_hac_prom~~ | ~~1~~ | ~~0~~ |
| | | | | |
| DNA | guppy_v6.5.7 | guppy_dna_r9.4.1_450bps_fast | 3 | 2 |
| DNA | guppy_v6.5.7 | guppy_dna_r9.4.1_450bps_fast_prom | 3 | 2 |
| DNA | guppy_v6.5.7 | guppy_dna_r9.4.1_450bps_hac | 3 | 2 |
| DNA | guppy_v6.5.7 | guppy_dna_r9.4.1_450bps_hac_prom | 3 | 2 |
| DNA | guppy_v6.5.7 | guppy_dna_r9.4.1_450bps_sup | 4 | 3 |
| DNA | guppy_v6.5.7 | guppy_dna_r9.4.1_450bps_sup_prom | 4 | 3 |
| | | | | |
| DNA | guppy_v6.5.7 | guppy_dna_r10.4.1_e8.2_400bps_fast | 2 | 1 |
| DNA | guppy_v6.5.7 | guppy_dna_r10.4.1_e8.2_400bps_fast_prom | 2 | 1 |
| DNA | guppy_v6.5.7 | guppy_dna_r10.4.1_e8.2_400bps_hac | 2 | 1 |
| DNA | guppy_v6.5.7 | guppy_dna_r10.4.1_e8.2_400bps_hac_prom | 2 | 1 |
| DNA | guppy_v6.5.7 | guppy_dna_r10.4.1_e8.2_400bps_sup | 2 | 1 |
| | | | | |
| RNA | guppy_v6.5.7 | guppy_rna_r9.4.1_70bps_fast | 1 | 0 |
| RNA | guppy_v6.5.7 | guppy_rna_r9.4.1_70bps_fast_prom | 1 | 0 |
| RNA | guppy_v6.5.7 | guppy_rna_r9.4.1_70bps_hac | 1 | 0 |
| RNA | guppy_v6.5.7 | guppy_rna_r9.4.1_70bps_hac_prom | 1 | 0 |

## Precomputed forward and reverse base shift values
The following precomputed forward and reverse base shift are available as profiles.
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19 changes: 1 addition & 18 deletions docs/reform.md
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Expand Up @@ -21,24 +21,7 @@ squigualiser reform -k ${KMER_LENGTH} -m ${SIG_MOVE_OFFSET} -c --bam basecalls.s

## Precomputed kmer lengths and signal move offsets

The following precomputed kmer length and signal move offset values are available as profiles in squigualiser.

These models were available in `ont-guppy_v6.3.7` and hence tested with `ont-guppy_v6.3.7`.

In the newer versions of `ont-guppy` we hope they don't change the model structure for the available ones.

We believe they will release models with proper names so that the old models are still identifiable.

We warmly welcome any pull request updating the following table with dorado models.

| profile | kmer length (k) | sig move offset (m) |
|------------------------------------|-----------------|---------------------|
| guppy_dna_r9.4.1_450bps_fast_prom | 3 | 2 |
| guppy_dna_r9.4.1_450bps_hac_prom | 3 | 2 |
| guppy_dna_r9.4.1_450bps_sup_prom | 4 | 3 |
| guppy_dna_r10.4.1_e8.2_400bps_fast | 1 | 0 |
| guppy_dna_r10.4.1_e8.2_400bps_hac | 1 | 0 |
| guppy_dna_r10.4.1_e8.2_400bps_sup | 1 | 0 |
Precomputed kmer lengths and signal move offsets can be found [here](profiles.md#precomputed-kmer-lengths-and-signal-moves-offsets).

If `reform` errors out with the message `"Error: specified profile is not found. Please run reform with -k 1 -s 0. Then run calculate_offsets.py and rerun reform with the recommended kmer_length and sig_move_offset."`, then the user is advised to run `calculate_offsets` subtool .
Information regarding `calcualte_offsets` is documented at [calculate_offsets](calculate_offsets.md).
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7 changes: 1 addition & 6 deletions src/plot_utils.py
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Expand Up @@ -143,12 +143,7 @@ def scale_signal(y, sig_scale, scale_params):
"kmer_model_dna_r9.4.1_450bps_6_mer": [-2, -3],
"kmer_model_rna_r9.4.1_70bps_5_mer": [-3, -1],
"kmer_model_dna_r10.4.1_e8.2_400bps_9_mer": [-6, -2],
"guppy_dna_r9.4.1_450bps_fast_prom": [0, 0],
"guppy_dna_r9.4.1_450bps_hac_prom": [0, 0],
"guppy_dna_r9.4.1_450bps_sup_prom": [0, 0],
"guppy_dna_r10.4.1_e8.2_400bps_fast": [0, 0],
"guppy_dna_r10.4.1_e8.2_400bps_hac": [0, 0],
"guppy_dna_r10.4.1_e8.2_400bps_sup": [0, 0]}
"corrected_at_reform": [0, 0]}
def list_profiles_base_shift():
# print(profile_dic)
print("{}\t{}\t{}".format("name", "base_shift_forward", "base_shift_reverse"))
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16 changes: 13 additions & 3 deletions src/reform.py
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Expand Up @@ -9,12 +9,22 @@
RNA_STRIDE = 10

profile_dic = {
"guppy_dna_r9.4.1_450bps_fast": [3, 2],
"guppy_dna_r9.4.1_450bps_fast_prom": [3, 2],
"guppy_dna_r9.4.1_450bps_hac": [3, 2],
"guppy_dna_r9.4.1_450bps_hac_prom": [3, 2],
"guppy_dna_r9.4.1_450bps_sup": [4, 3],
"guppy_dna_r9.4.1_450bps_sup_prom": [4, 3],
"guppy_dna_r10.4.1_e8.2_400bps_fast": [1, 0],
"guppy_dna_r10.4.1_e8.2_400bps_hac": [1, 0],
"guppy_dna_r10.4.1_e8.2_400bps_sup": [1, 0]}
"guppy_dna_r10.4.1_e8.2_400bps_fast": [2, 1],
"guppy_dna_r10.4.1_e8.2_400bps_fast_prom": [2, 1],
"guppy_dna_r10.4.1_e8.2_400bps_hac": [2, 1],
"guppy_dna_r10.4.1_e8.2_400bps_hac_prom": [2, 1],
"guppy_dna_r10.4.1_e8.2_400bps_sup": [2, 1],
"guppy_rna_r9.4.1_70bps_fast": [1, 0],
"guppy_rna_r9.4.1_70bps_fast_prom": [1, 0],
"guppy_rna_r9.4.1_70bps_hac": [1, 0],
"guppy_rna_r9.4.1_70bps_hac_prom": [1, 0]
}

def list_profiles():
# print(profile_dic)
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