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Guppy2 models

Jun 28, 2021. The ONT model trained with Guppy3 and Guppy4 data performed even worse than Clair on Guppy2 data. We collected and trained a model specially for reads basecalled using Guppy2 or prior. The new model is available here (first released with v0.1-r4). Below are some benchmarks (GIAB v4.2.1) showing a signficiant improvement when using the correct model for your data.

Model/Caller Testing
Dataset		 Overall-
Precision		 Overall-
Recall		 Overall-
F1		 SNP-
Precision		 SNP-
Recall		 SNP-
F1		 Indel-
Precision		 Indel-
Recall		 Indel-
F1
Guppy2 model Guppy2 HG002 chr20 ~64x 98.365% 92.406% 95.292% 99.541% 99.080% 99.310% 85.847% 50.107% 63.279%
Guppy3,4 model Guppy2 HG002 chr20 ~64x 72.329% 90.896% 80.556% 99.337% 98.536% 98.935% 14.648% 42.475% 21.784%
Guppy2 model Guppy4 HG002 chr20 ~64x 86.897% 92.707% 89.708% 97.983% 99.579% 98.775% 35.773% 49.156% 41.410%
Guppy3,4 model Guppy4 HG002 chr20 ~64x 98.512% 94.601% 96.517% 99.759% 99.749% 99.754% 87.586% 61.976% 72.588%
Clair ONT model Guppy2 HG002 chr20 ~64x 98.007% 87.739% 92.590% 99.290% 96.448% 97.848% 79.013% 32.552% 46.108%

Use the Guppy2 model

INPUT_DIR="[YOUR_INPUT_FOLDER]"           # e.g. /home/user1/input (absolute path needed)
OUTPUT_DIR="[YOUR_OUTPUT_FOLDER]"         # e.g. /home/user1/output (absolute path needed)
THREADS="[MAXIMUM_THREADS]"               # e.g. 8

docker run -it \
  -v ${INPUT_DIR}:${INPUT_DIR} \
  -v ${OUTPUT_DIR}:${OUTPUT_DIR} \
  hkubal/clair3:latest \
  /opt/bin/run_clair3.sh \
  --bam_fn=${INPUT_DIR}/input.bam \       ## change your bam file name here
  --ref_fn=${INPUT_DIR}/ref.fa \          ## change your reference name here
  --threads=${THREADS} \                  ## maximum threads to be used
  --platform="ont" \                       
  --model_path="/opt/models/r941_prom_hac_g238" \  
  --output=${OUTPUT_DIR}                  ## absolute output path prefix

Check Usage for more options.

Guppy2 training data

Reference Sample Aligner Coverage Basecaller link
GRCh38 HG001 minimap2 ~124x Guppy v2.2.3 -
GRCh38 HG002 minimap2 ~64x Guppy v2.3.8 link
GRCh38 HG003 minimap2 ~91x Guppy v2.3.8 link
GRCh38 HG004 minimap2 ~90x Guppy v2.3.8 link