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Additional file 4 of A comprehensive investigation of metagenome assembly by linked-read sequencing

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journal contribution
posted on 2020-11-12, 04:37 authored by Lu Zhang, Xiaodong Fang, Herui Liao, Zhenmiao Zhang, Xin Zhou, Lijuan Han, Yang Chen, Qinwei Qiu, Shuai Cheng Li
Additional file 4: Figure S1. Distributions of bin completeness and contamination of SCF- and SCR- of human gut microbiome data. Figure S2. Upset plots for the shared genus (A: SCF-, C: SCR-) and species (B: SCF-, D: SCR-) of different subsampling datasets. Figure S3. Comparison of the contig NG50 and NGA50 between Illumina short-reads (Illumina) and 10x linked-reads (MSC1) from the mock community. Figure S4. Comparison of the contig NG50 and NGA50 between PacBio CCS reads (CCS) and 10x linked-reads (MSC1) from the mock community. Figure S5. Parameter distributions of linked-read sequencing from human gut microbiome. PDF: probability density function; CDF: cumulative density function. Figure S6. Parameter distributions of linked-read sequencing from human genome (NA24385). PDF: probability density function; CDF: cumulative density function. Figure S7. Workflow of LRTK-SIM to simulate linked-reads for microbial genomes with uneven depth. Figure S8. Workflow of linked-reads metagenome assembly on simulated 10x linked-reads. Figure S9. Workflow for evaluating and comparing different metagenome assemblies. Figure S10. The distributions of genomic coverage and read depth for the microbes in human microbiome project according to the alignment of the linked-reads from human gut microbiome. CDF: cumulative density function. Supplementary Note: 1. Complexity and statistics for linked-reads from human gut microbiome. 2. Command lines adopted for the analysis.

Funding

Research Grants Council, University Grants Committee Natural Science Foundation of Guangdong Province

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