squigulator

Parameter profiles

Inspired by parameter presets in Minimap2, Squigulator has parameter profiles/presets that can be used via the -x option. This provides the user with a convenient way to simulate different chemistries and flowcells, without having to use advanced parameters.

Parameter profiles are currently available for R9.4.1, R10.4.1 amd RNA004. More profiles will be added in future when new nanopore chemistries are introduced.

R9 profiles

Following profiles are available for R9.4.1.

These profile sets the following advanced parameters in squigulator.

Parameter dna-r9-min dna-r9-prom rna-r9-min rna-r9-prom
digitisation 8192 2048 8192 2048
sample-rate 4000 4000 3012 3000
bps 450 450 70 70
range 1443.030273 748.5801 1126.47 548.788269
offset-mean 13.7222605 -237.4102 4.65491888 -231.9440589
Offset-std 10.25279688 14.1575 4.115262472 12.87185278
median-before-mean 200.815801 214.2890337 242.6584118 238.5286796
median-before-std 20.48933762 18.0127916 10.60230888 21.1871794
dwell-mean 9.0 9.0 43.0 43.0
dwell-std 4.0 4.0 35.0 35.0

R10 and RNA004 profiles

Following profiles are available for R10.4.1 and RNA004.

These profile sets the following advanced parameters in squigulator.

Parameter dna-r10-min dna-r10-prom rna004-min rna004-prom
digitisation 8192 2048 8192 2048
sample-rate 4000 4000 4000 4000
bps 400 400 130 130
range 1536.598389 281.345551 1437.976685 299.432068
offset-mean 13.380569389 -127.5655735 12.47686423863 -259.421128
offset-std 16.311471649 19.377283387665 10.442126577137 16.010841823643
median-before-mean 202.154074388 189.87607393756 205.08496731088 189.87607393756
median-before-std 13.406139242 15.788097978713 8.6671292866233 15.788097978713
dwell-mean 10.0 10.0 31.0 31.0
dwell-std 4.0 4.0 0.0 0.0

Determining parameters for a profile

This section briefly describes how these parameter profiles are created for a given flow-cell chemistry. Following requirements and assumptions must be met.

Now let us see how the the parameters are deduced.

  slow5tools skim -t40 reads_500k.blow5 | awk -v c="median_before" 'NR==1{for (i=1; i<=NF; i++) if ($i==c){p=i; break};} {if ($p!=".") print $p}' | tail -n+2 | datamash mean 1 sstdev 1
  205.63935594369 8.3994882799157