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Training Data

ONT

Sample Reference Aligner Coverage Basecaller link
HG001 GRCh38_no_alt minimap2 58.1 Guppy v4.2.2 link
HG001 GRCh38_no_alt minimap2 35.3 Guppy v4.2.2 link
HG002 GRCh38_no_alt minimap2 432.4 Guppy v4.2.2 link
HG002 GRCh38_no_alt minimap2 49.0 Guppy v3.6.0 link
HG003 GRCh38_no_alt minimap2 85.0 Guppy v4.2.2 link
HG003 GRCh38_no_alt minimap2 84.8 Guppy v3.6.0 link
HG004 GRCh38_no_alt minimap2 87.5 Guppy v4.2.2 link
HG004 GRCh38_no_alt minimap2 87.4 Guppy v3.6.0 link
HG005 GRCh38_no_alt minimap2 57.0 Guppy v4.2.2 link

PacBio HiFi

Sample Reference Aligner Coverage Chemistry Link
HG001 GRCh38_no_alt pbmm2 29.2 CCS Sequel II, chemistry 1.0 link
HG002 GRCh38_no_alt pbmm2 32.0 CCS-15kb Sequel II, chemistry 0.9 link
HG002 GRCh38_no_alt pbmm2 53.3 CCS-20kb Sequel II, chemistry 2.0 link
HG002 GRCh38_no_alt pbmm2 34.9 CCS-15kb Sequel II, chemistry 2.0 link
HG003 GRCh38_no_alt pbmm2 34.3 CCS-15kb Sequel II, chemistry 2.0 link
HG004 GRCh38_no_alt pbmm2 34.3 CCS-15kb Sequel II, chemistry 2.0 link
HG004 GRCh38_no_alt pbmm2 60.5 CCS-20kb Sequel II, chemistry 2.0 link
HG004 GRCh38_no_alt pbmm2 20.8 CCS-15kb Sequel II, chemistry 2.0 link
HG005 GRCh38_no_alt pbmm2 31.7 CCS Sequel II, chemistry 1.0 link

Illumina

Sample Reference Aligner Coverage Sequencer Link
HG001 GRCh38 BWA-MEM 41.5 HiSeqX link
HG001 GRCh38 BWA-MEM 46.3 NovaSeq link
HG002 GRCh38_no_alt NovoAlign 276.3 HiSeqX link
HG002 GRCh38 BWA-MEM 38.8 HiSeqX link
HG002 GRCh38 BWA-MEM 42.1 HiSeqX link
HG002 GRCh38 BWA-MEM 49.8 NovaSeq link
HG003 GRCh38 BWA-MEM 39.1 NovaSeq link
HG004 GRCh38 BWA-MEM 39.3 NovaSeq link
HG004 GRCh38 BWA-MEM 42.1 HiSeqX link
HG004 GRCh38 BWA-MEM 46.4 NovaSeq link
HG005 GRCh38 BWA-MEM 43.8 HiSeqX link
HG005 GRCh38 BWA-MEM 42.4 NovaSeq link

Pre-trained Model

Download models from here or click on the links below.

In a docker installation, models are in /opt/models/. In a bioconda installation, models are in {CONDA_PREFIX}/bin/models/.

Model name Platform Training samples Included in the bioconda package Included in the docker image Release Date Basecaller File Link
r941_prom_hac_g360+g422 ONT HG001,2,4,5 Yes Yes 1 20210517 Guppy3,4 r941_prom_hac_g360+g422.tar.gz Download
r941_prom_hac_g360+g422_1235 ONT HG001,2,3,5 1 20210517 Guppy3,4 r941_prom_hac_g360+g422_1235.tar.gz Download
r941_prom_sup_g506 ONT Base model: HG001,2,4,5 (Guppy3,4)
Fine-tuning data: HG002 (Guppy5_sup)		 Yes Yes 1 20210609 Guppy5 r941_prom_sup_g506.tar.gz Download
r941_prom_hac_g238 ONT HG001,2,3,4 Yes 1 20210627 Guppy2 r941_prom_hac_g238.tar.gz Download
hifi PacBio HiFi HG001,2,4,5 Yes Yes 1 20210517 NA hifi.tar.gz Download
ilmn Illumina HG001,2,4,5 Yes Yes 1 20210517 NA ilmn.tar.gz Download