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Genome assembly analysis with DeepConsensus reads.

DeepConsensus improves the consensus accuracy and yield of the PacBio CCS reads which downstream can improve the quality of genome analysis. To assess the 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, 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

We performed genome assembly on reads from two PacBio SMRT Cells with insert sizes of 16kb and 24kb.

Table 1: HG002 assembly metrics with 2 SMRT Cells of PacBio CCS reads with 16kb insert size.

Method Version Assembly N50 hap-1 QV hap-2 QV Mean QV
HiFi - 32253089 51.878 51.731 51.8045
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.

Method Version Assembly N50 hap-1 QV hap-2 QV Mean QV
HiFi - 30789663 49.878 49.847 49.8625
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

Here we describe the methods used to perform the assembly and to estimate the quality of the assemblies.

Assembly

We performed the genome assemblies with hifiasm v0.16.1 assembler using the following command:

hifiasm -o OUTPUT_DIR/OUTPUT_PREFIX -t NUMBER_PROCESSES FASTQ_FILE

Reference free QV estimation

We used YAK v0.1-r56 to evaluate the assembly quality. YAK uses the k-mer distribution observed in short-reads (Illumina) to evaluate the quality of the sequence present in the assembly. We used the following command for YAK:

yak qv -t NUMBER_PROCESSES \
-p -K 3.2g -l 100k KMER_DB ASSEMBLY_FASTA > OUTPUT_qv.txt

Data availability

The data used for this analysis is available publicly.

PacBio CCS reads (FASTQ)

Sample Insert size Method Version Location
HG002 16kb HiFi - gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.hifi.q20.fastq
HG002 16kb DeepConsensus v0.2 gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.dc.v0.2.q20.fastq.gz
HG002 16kb DeepConsensus v0.3 gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/fastqs/HG002_16kb_2SMRT_cells.dc.v0.3.q20.fastq.gz
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

Sample Insert size Method Version Location
HG002 16kb HiFi - gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/hifiasm_outputs/HG002_16kb_2SMRT_cells_hifi_q20/
HG002 16kb DeepConsensus v0.2 gs://brain-genomics-public/research/deepconsensus/data/v0.3/assembly_analysis/hifiasm_outputs/HG002_16kb_2SMRT_cells_dc_v0.2_q20/
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/