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Update assembly metrics for v1.2.
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anastasiyabl authored and Copybara-Service committed Feb 15, 2023
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12 changes: 10 additions & 2 deletions docs/assembly_metrics.md
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Expand Up @@ -6,8 +6,9 @@ improvement we can achieve by using DeepConsensus reads for genome assembly, we
used `hifiasm (v0.16.1)` assembler to assemble the HG002 sample and used `YAK
v0.1-r56` to assess the quality of the assembly.

Notably, the `DeepConsensus v0.3, v1.0 and v1.1` models are trained on the `T2T
v2.0` assembly of CHM13, so HG002 is a held out sample used for this analysis.
Notably, the `DeepConsensus v0.3, v1.0, v1.1 and v1.2` models are trained on the
`T2T v2.0` assembly of CHM13 (with `v1.2` being additionally trained on maize),
so HG002 is a held out sample used for this analysis.

## Results

Expand All @@ -24,6 +25,7 @@ DeepConsensus | v0.2 | 34721278 | 52.74 | 52.526 | 52.633
DeepConsensus | v0.3 | 35794972 | 52.819 | 52.79 | 52.8045
DeepConsensus | v1.0 | 33141115 | 53.092 | 53.033 | 53.0625
DeepConsensus | v1.1 | 34129352 | 52.930 | 52.910 | 52.92
DeepConsensus | v1.2 | 36019127 | 53.105 | 53.056 | 53.0805

**Table 2: HG002 assembly metrics with 2 SMRT Cells of PacBio CCS reads with
24kb insert size.**
Expand All @@ -35,6 +37,8 @@ DeepConsensus | v0.2 | 33130436 | 51.285 | 51.154 | 51.2195
DeepConsensus | v0.3 | 31478064 | 51.478 | 51.446 | 51.462
DeepConsensus | v1.0 | 31480574 | 51.932 | 51.775 | 51.8535
DeepConsensus | v1.1 | 34046473 | 52.001 | 51.923 | 51.962
DeepConsensus | v1.2 | 34052833 | 52.223 | 51.975 | 52.099


## Methods

Expand Down Expand Up @@ -76,11 +80,13 @@ HG002 | 16kb | DeepConsensus | v0.3 | gs://brain-genomics-public/rese
HG002 | 16kb | DeepConsensus | v0.3 | gs://brain-genomics-public/research/deepconsensus/data/v1.0/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.dc.v1.0.q20.fastq.gz
HG002 | 16kb | DeepConsensus | v1.0 | gs://brain-genomics-public/research/deepconsensus/data/v1.0/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.dc.v1.0.q20.fastq.gz
HG002 | 16kb | DeepConsensus | v1.1 | gs://brain-genomics-public/research/deepconsensus/data/v1.1/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.dc.v1.1.q20.fastq.gz
HG002 | 16kb | DeepConsensus | v1.2 | gs://brain-genomics-public/research/deepconsensus/data/v1.2/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.dc.v1.2.q20.fastq.gz
HG002 | 24kb | HiFi | - | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.hifi.q20.fastq
HG002 | 24kb | DeepConsensus | v0.2 | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.dc.v0.2.q20.fastq.gz
HG002 | 24kb | DeepConsensus | v0.3 | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.dc.v0.3.q20.fastq.gz
HG002 | 24kb | DeepConsensus | v1.0 | gs://brain-genomics-public/research/deepconsensus/data/v1.0/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.dc.v1.0.q20.fastq.gz
HG002 | 24kb | DeepConsensus | v1.1 | gs://brain-genomics-public/research/deepconsensus/data/v1.1/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.dc.v1.1.q20.fastq.gz
HG002 | 24kb | DeepConsensus | v1.2 | gs://brain-genomics-public/research/deepconsensus/data/v1.2/assembly_analysis/fastqs/HG002_24kb_2SMRT_cells.dc.v1.2.q20.fastq.gz

### Assembly outputs

Expand All @@ -91,8 +97,10 @@ HG002 | 16kb | DeepConsensus | v0.2 | gs://brain-genomics-public/rese
HG002 | 16kb | DeepConsensus | v0.3 | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/hifiasm_outputs/HG002_16kb_2SMRT_cells_dc_v0.3_q20/
HG002 | 16kb | DeepConsensus | v1.0 | gs://brain-genomics-public/research/deepconsensus/data/v1.0/assembly_analysis/hifiasm_outputs/HG002_16kb_2SMRT_cells_dc_v1.0_q20/
HG002 | 16kb | DeepConsensus | v1.1 | gs://brain-genomics-public/research/deepconsensus/data/v1.1/assembly_analysis/hifiasm_outputs/HG002_16kb_2SMRT_cells_dc_v1.1_q20/
HG002 | 16kb | DeepConsensus | v1.2 | gs://brain-genomics-public/research/deepconsensus/data/v1.2/assembly_analysis/hifiasm_outputs/HG002_16kb_2SMRT_cells_dc_v1.2_q20/
HG002 | 24kb | HiFi | - | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/hifiasm_outputs/HG002_24kb_2SMRT_cells_hifi_q20/
HG002 | 24kb | DeepConsensus | v0.2 | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/hifiasm_outputs/HG002_24kb_2SMRT_cells_dc_v0.2_q20/
HG002 | 24kb | DeepConsensus | v0.3 | gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/hifiasm_outputs/HG002_24kb_2SMRT_cells_dc_v0.3_q20/
HG002 | 24kb | DeepConsensus | v1.0 | gs://brain-genomics-public/research/deepconsensus/data/v1.0/assembly_analysis/hifiasm_outputs/HG002_24kb_2SMRT_cells_dc_v1.0_q20/
HG002 | 24kb | DeepConsensus | v1.1 | gs://brain-genomics-public/research/deepconsensus/data/v1.1/assembly_analysis/hifiasm_outputs/HG002_24kb_2SMRT_cells_dc_v1.1_q20/
HG002 | 24kb | DeepConsensus | v1.2 | gs://brain-genomics-public/research/deepconsensus/data/v1.2/assembly_analysis/hifiasm_outputs/HG002_24kb_2SMRT_cells_dc_v1.2_q20/

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