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updated README
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@JasonCLEI
JasonCLEI committed Nov 29, 2024
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Expand Up @@ -89,19 +89,23 @@ Check [Usage](#Usage) for more options.

ClairS-TO trained both Affirmative and Negational models using GIAB samples, and carry on benchmarking on HCC1395 tumor sample dataset. All models were trained with chr20 excluded (including only chr1-19, 21, 22).

| Platform | Model name | Chemistry /Instruments | Basecaller | Latest update | Option (`-p/--platform`) | Reference | Aligner |
|:-----------------:|:-------------------------:|:--------------------------------:|:----------:|:-------------:|:------------------------------:|:-------------:|:----------:|
| ONT <sup>1</sup> | r1041_e82_400bps_sup_v420 | R10.4.1, 5khz | Dorado SUP | Sep. 30, 2024 | `ont_r10_dorado_sup_5khz_ssrs` | GRCh38_no_alt | Minimap2 |
| ONT <sup>1</sup> | r1041_e82_400bps_sup_v420 | R10.4.1, 5khz | Dorado SUP | Nov. 10, 2023 | `ont_r10_dorado_sup_5khz_ss` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_sup_v420 | R10.4.1, 5khz | Dorado SUP | Nov. 10, 2023 | `ont_r10_dorado_sup_5khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_sup_v410 | R10.4.1, 4khz | Dorado SUP | Nov. 10, 2023 | `ont_r10_dorado_sup_4khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_hac_v410 | R10.4.1, 4khz | Dorado HAC | Jan. 19, 2024 | `ont_r10_dorado_hac_4khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_sup_g615 | R10.4.1, 4khz | Guppy6 SUP | Nov. 10, 2023 | `ont_r10_guppy_sup_4khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_hac_g657 | R10.4.1, 5khz | Guppy6 HAC | Jan. 21, 2024 | `ont_r10_guppy_hac_5khz` | GRCh38_no_alt | Minimap2 |
| Illumina | ilmn | NovaSeq/HiseqX | - | Nov. 10, 2023 | `ilmn` | GRCh38 | BWA-MEM |
| PacBio HiFi | hifi_revio | Revio with SMRTbell prep kit 3.0 | - | Nov. 10, 2023 | `hifi_revio` | GRCh38_no_alt | Minimap2 |

**Caveats <sup>1</sup>**: Starting from v0.3.0 version, ClairS-TO will provide two model types. `ssrs` is a model trained initially with synthetic samples and then real samples augmented (e.g., `ont_r10_dorado_sup_5khz_ssrs`), `ss` is a model trained from synthetic samples (e.g., `ont_r10_dorado_sup_5khz_ss`). The `ssrs` model provides better performance and fits most usage scenarios. `ss` model can be used when missing a cancer-type in model training is a concern. In v0.3.0, four real cancer cell-line datasets (HCC1937, HCC1954, H1437, and H2009) covering two cancer types (breast cancer, lung cancer) published by [Park et al.](https://www.biorxiv.org/content/10.1101/2024.08.16.608331v1) were used for `ssrs` model training.
| Platform | Model name | Chemistry /Instruments | Basecaller | Latest update | Option (`-p/--platform`) | Reference | Aligner |
|:------------------------------------:|:-------------------------:|:--------------------------------:|:----------:|:-------------:|:---------------------------------:|:-------------:|:----------:|
| ONT <sup>1</sup> | r1041_e82_400bps_sup_v420 | R10.4.1, 5khz | Dorado SUP | Nov. 20, 2024 | `ont_r10_dorado_sup_5khz_ssrs` | GRCh38_no_alt | Minimap2 |
| ONT <sup>1</sup> | r1041_e82_400bps_sup_v420 | R10.4.1, 5khz | Dorado SUP | Nov. 10, 2023 | `ont_r10_dorado_sup_5khz_ss` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_sup_v420 | R10.4.1, 5khz | Dorado SUP | Nov. 10, 2023 | `ont_r10_dorado_sup_5khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_sup_v410 | R10.4.1, 4khz | Dorado SUP | Nov. 10, 2023 | `ont_r10_dorado_sup_4khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_hac_v410 | R10.4.1, 4khz | Dorado HAC | Jan. 19, 2024 | `ont_r10_dorado_hac_4khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_sup_g615 | R10.4.1, 4khz | Guppy6 SUP | Nov. 10, 2023 | `ont_r10_guppy_sup_4khz` | GRCh38_no_alt | Minimap2 |
| ONT | r1041_e82_400bps_hac_g657 | R10.4.1, 5khz | Guppy6 HAC | Jan. 21, 2024 | `ont_r10_guppy_hac_5khz` | GRCh38_no_alt | Minimap2 |
| Illumina <sup>1</sup> | ilmn | NovaSeq/HiseqX | - | Nov. 20, 2024 | `ilmn_ssrs` | GRCh38 | BWA-MEM |
| Illumina <sup>1</sup> | ilmn | NovaSeq/HiseqX | - | Nov. 10, 2023 | `ilmn_ss` | GRCh38 | BWA-MEM |
| Illumina | ilmn | NovaSeq/HiseqX | - | Nov. 10, 2023 | `ilmn` | GRCh38 | BWA-MEM |
| PacBio HiFi <sup>1</sup> | hifi_revio | Revio with SMRTbell prep kit 3.0 | - | Nov. 20, 2024 | `hifi_revio_ssrs` | GRCh38_no_alt | Minimap2 |
| PacBio HiFi <sup>1</sup> | hifi_revio | Revio with SMRTbell prep kit 3.0 | - | Nov. 10, 2023 | `hifi_revio_ss` | GRCh38_no_alt | Minimap2 |
| PacBio HiFi | hifi_revio | Revio with SMRTbell prep kit 3.0 | - | Nov. 10, 2023 | `hifi_revio` | GRCh38_no_alt | Minimap2 |

**Caveats <sup>1</sup>**: Starting from v0.3.0 version, ClairS-TO will provide two model types. `ssrs` is a model trained initially with synthetic samples and then real samples augmented (e.g., `ont_r10_dorado_sup_5khz_ssrs`, `ilmn_ssrs`, `hifi_revio_ssrs`), `ss` is a model trained from synthetic samples (e.g., `ont_r10_dorado_sup_5khz_ss`, `ilmn_ss`, `hifi_revio_ss`). The `ssrs` model provides better performance and fits most usage scenarios. `ss` model can be used when missing a cancer-type in model training is a concern. In v0.3.0, four real cancer cell-line datasets (HCC1937, HCC1954, H1437, and H2009) covering two cancer types (breast cancer, lung cancer) published by [Park et al.](https://www.biorxiv.org/content/10.1101/2024.08.16.608331v1) were used for `ssrs` model training.

------

Expand All @@ -123,7 +127,7 @@ docker run -it \
--tumor_bam_fn ${INPUT_DIR}/tumor.bam \ ## use your tumor bam file name here
--ref_fn ${INPUT_DIR}/ref.fa \ ## use your reference file name here
--threads ${THREADS} \ ## maximum threads to be used
--platform ${PLATFORM} \ ## options: {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, hifi_revio}
--platform ${PLATFORM} \ ## options: {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_dorado_sup_5khz_ss, ont_r10_dorado_sup_5khz_ssrs, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, ilmn_ss, ilmn_ssrs, hifi_revio, hifi_revio_ss, hifi_revio_ssrs}
--output_dir ${OUTPUT_DIR} ## output path prefix
```

Expand Down Expand Up @@ -153,7 +157,7 @@ singularity exec \
--tumor_bam_fn ${INPUT_DIR}/tumor.bam \ ## use your tumor bam file name here
--ref_fn ${INPUT_DIR}/ref.fa \ ## use your reference file name here
--threads ${THREADS} \ ## maximum threads to be used
--platform ${PLATFORM} \ ## options: {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, hifi_revio}
--platform ${PLATFORM} \ ## options: {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_dorado_sup_5khz_ss, ont_r10_dorado_sup_5khz_ssrs, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, ilmn_ss, ilmn_ssrs, hifi_revio, hifi_revio_ss, hifi_revio_ssrs}
--output_dir ${OUTPUT_DIR} \ ## output path prefix
--conda_prefix /opt/micromamba/envs/clairs-to
```
Expand Down Expand Up @@ -256,7 +260,7 @@ docker run -it hkubal/clairs-to:latest /opt/bin/run_clairs_to --help
--tumor_bam_fn ${INPUT_DIR}/tumor.bam \ ## use your tumor bam file name here
--ref_fn ${INPUT_DIR}/ref.fa \ ## use your reference file name here
--threads ${THREADS} \ ## maximum threads to be used
--platform ${PLATFORM} \ ## options: {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, hifi_revio}
--platform ${PLATFORM} \ ## options: {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_dorado_sup_5khz_ss, ont_r10_dorado_sup_5khz_ssrs, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, ilmn_ss, ilmn_ssrs, hifi_revio, hifi_revio_ss, hifi_revio_ssrs}
--output_dir ${OUTPUT_DIR} ## output path prefix

## Final SNV output VCF file: output/snv.vcf.gz
Expand All @@ -272,7 +276,7 @@ docker run -it hkubal/clairs-to:latest /opt/bin/run_clairs_to --help
-R, --ref_fn FASTA Reference file input. The input file must be samtools indexed.
-o, --output_dir OUTPUT_DIR VCF output directory.
-t, --threads THREADS Max threads to be used.
-p, --platform PLATFORM Select the sequencing platform of the input. Possible options {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_dorado_sup_5khz_ss, ont_r10_dorado_sup_5khz_ssrs, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, hifi_revio}.
-p, --platform PLATFORM Select the sequencing platform of the input. Possible options {ont_r10_dorado_sup_4khz, ont_r10_dorado_hac_4khz, ont_r10_dorado_sup_5khz, ont_r10_dorado_sup_5khz_ss, ont_r10_dorado_sup_5khz_ssrs, ont_r10_guppy_sup_4khz, ont_r10_guppy_hac_5khz, ilmn, ilmn_ss, ilmn_ssrs, hifi_revio, hifi_revio_ss, hifi_revio_ssrs}.
```

**Commonly used parameters:**
Expand Down

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