Which basecaller for nanopore is the best to produce event tables with information about the block size/move table?

Question

I previously used albacore version 2.3.1 to make initial move tables, but then I re-squiggle using Tombo version 1.5.1 to fix the errors.

Example of move table produced by albacore, in which all the moves have the same size:

When it is re-squiggled by Tombo (which produces variable length moves/blocks):

I am starting a new project, and I can repeat the same pipeline, however, my concern is that albacore version 2.3.1 is too old now and I was wondering to ask if there are better pipelines/software for base-calling that produces initial move tables so that I can build on top of.

Answer 1

ONT's newest basecaller, Dorado, can do this for SAM output with the --emit-moves argument. It was added in this commit.

Dorado can be downloaded from here:

https://github.com/nanoporetech/dorado

Here's an example command line:

$ ~/install/dorado/dorado-0.2.1-linux-x64/bin/dorado basecaller --emit-moves \
  ~/install/dorado/dorado-0.2.1-linux-x64/[email protected] DAE_pod5 | \
  samtools view -b - > called_DAE_gDNA_reads_all.bam

And a few lines of example output:

@HD     VN:1.6  SO:unknown
@PG     ID:basecaller   PN:dorado       VN:0.2.1+c70423e        CL:dorado basecaller --emit-moves /home/minion/install/dorado/dorado-0.2.1-linux-x64/[email protected] DAE_pod5
@PG     ID:samtools     PN:samtools     PP:basecaller   VN:1.10 CL:samtools view -b -
@PG     ID:samtools.1   PN:samtools     PP:samtools     VN:1.10 CL:samtools view -h called_DAE_gDNA_reads_all.bam
@RG     ID:460fc479-3b30-4ed5-801f-a82bbe556101_dna_r10.4.1_e8.2_260bps_sup@v4.1.0      PU:PAK83314     PM:     DT:2023-02-08T10:22:53.256+00:00        PL:ONT  DS:[email protected] runid=460fc479-3b30-4ed5-801f-a82bbe556101 LB:DAE_gDNA     SM:DAE_gDNA
@RG     ID:227379b1-c5fc-465d-9e24-eb771133f11e_dna_r10.4.1_e8.2_260bps_sup@v4.1.0      PU:PAK83314     PM:     DT:2023-02-08T20:28:34.34+00:00 PL:ONT  DS:[email protected] runid=227379b1-c5fc-465d-9e24-eb771133f11e LB:no_sample    SM:no_sample
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002e48ca-84bf-4419-8370-943d1ca3ac64    4       *       0       0       *       *       0       107     TATGTCTAACTTACTTCGTTCAGTTGTGAAAACTGGGTGTTTAACCTTTGATTCTATCGTGTTTCCCTAGTTTTCGCATTTGACGTGAAACGCTTTCACATTTTGGT     &&'''&%%%%((((*+)***())((')&%%%%$%%%'--,,,,-6996/,+-5ABBBCCFBCE>88:1764424/--,,--&%$$%*08??;;;;<B<:((('()//     qs:i:9  du:f:0.92975    ns:i:3719       ts:i:10 mx:i:4  ch:i:1058       st:Z:2023-02-09T07:07:08.905+00:00      rn:i:62167      f5:Z:PAK83314_fail_unclassified_227379b1_ea81734c_853.pod5      sm:f:85.094     sd:f:23.944     sv:Z:quantile   RG:Z:227379b1-c5fc-465d-9e24-eb771133f11e_dna_r10.4.1_e8.2_260bps_sup@v4.1.0    mv:B:c,5,1,0,0,0,0,0,0,1,0,0,0,0,0,1,1,0,0,0,0,0,1,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,1,1,1,0,1,0,1,0,0,1,0,0,1,0,1,1,0,0,1,0,1,0,0,0,0,1,0,0,1,0,1,0,0,1,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,1,0,1,0,0,1,0,1,0,1,1,0,1,0,0,0,0,0,1,0,0,1,0,0,1,0,1,0,1,0,0,1,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,1,0,0,0,0,0,0,1,0,1,0,1,0,0,1,0,1,0,0,1,0,1,0,0,1,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,1,0,1,0,1,1,0,1,0,0,1,0,1,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,1,0,1,0,1,0,1,0,1,0,0,1,0,1,0,0,0,1,0,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,0,1,0,0,1,0,0,1,0,0,0,0,1,0,1,0,0,1,0,0,0,1,0,0
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Based on the commit, the move table is attached to the mv tag for each read, indicating an array of 8-bit signed integers (represented as comma-separated values in the SAM output). I'd guess (based on how the calling has worked in the past) that these represent strides comprising a fixed number of consecutive samples, so (as before) it'll need correction to convert the stride width to variable width events.

For the model I'm using here, my guess from the model toml file is that the stride width is 5:

$ grep -B 8 stride ~/install/dorado/dorado-0.2.1-linux-x64/[email protected]/config.toml 
[encoder]
type = "serial"
[[encoder.sublayers]]
type = "convolution"
insize = 1
size = 16
bias = true
winlen = 5
stride = 1
--
max = 3.5

[[encoder.sublayers]]
type = "convolution"
insize = 16
size = 16
bias = true
winlen = 5
stride = 1
--
max = 3.5

[[encoder.sublayers]]
type = "convolution"
insize = 16
size = 1024
bias = true
winlen = 19
stride = 5
```