Additional file 4 of A single-stranded based library preparation method for virome characterization
Creators: name: Zhai, Xichuan
name: Gobbi, Alex
name: Kot, Witold
name: Krych, Lukasz
name: Nielsen, Dennis Sandris
name: Deng, Ling
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4. Supplementary Table S1-S11. TableS1: Summary of DNA genome sequences. Top table: Relative abundance and coverage of phage genomes in libraries from DNA mock communities (Mock A, Mock B and Mock C) with T4 genome. The relative abundance of each genome was calculated based on its coverage by using bowtie2 alignment with our customed database (https://github.com/XC-Zhai/SSLR/tree/main/Customed_db). For comparing the efficiency of different methods for each group of phages (i.e., dsDNA and ssDNA), relative abundance of two type genomes were computed from this table (by dividing the value for each phage by the sum for the group). Middle table: The average coverage for each genome from each library preparation method. Bottom table: similar to top table without T4 genome. TableS2: Comparisons of cost and effectiveness of Mock virome library preparation method. This comparison only considers the library preparation step for DNA virome. TableS3: Overview of metavirome sequencing for the DNA phage mock community. Statistics from assembly before and after quality checks with CheckV, vibrant and virsorter2. Contigs from each library prepared methods were evaluated by quality checks with CheckV, vibrant and virsorter2 and then subjected to the Quast for quality assessment of assembled contigs. The theatrical statistics of mock community were also subjected to Quast and bolded at the bottom of table (in yellow background). TableS4: Summary of contigs hits to the customed mock database. The quality-checked contigs were subjected to the customed database and the hit number was counted and listed in the table. TableS5: Summary of DNA genome sequences with interested modified genomes (T4 and T4-c). T4 is a highly modified genome, T4-c has lower modification compared to T4 genome. TableS6: Summary of DNA/RNA genome sequences prepared with SSLR method. Relative abundance and coverage of phage genomes in libraries from DNA/RNA mock communities (Mock D, Mock E and Mock F) with different treatments (heat, no heat, DMSO and no DMSO). The relative abundance of each genome was calculated based on its coverage by using bowtie2 alignment with our customed database. For comparing the efficiency of different treatments for each type of phage genome (DNA and RNA), relative abundance of two type genomes (DNA or RNA) were calculated from this table (by dividing the value for each phage by the sum for the genome types). Middle table: The average coverage for each genome from each library preparation method. The average coverage for each genome from each treatment method is listed in the bottom table. TableS7: Taxonomic classification of fecal metavirome sequencing reads into the categories viral, human, bacterial, and unknown origin. To check the presence of non-viral DNA sequences, 50,000 random forward reads were used according to their match to a range of viral, bacterial, and human reference database of Kaiju 1.8.2. TableS8: Relative abundance of fecal virome prepared with 5 different library strategies at taxonomy of family level (support data for Fig.5B) and the overall alignment rate of different library preparation methods based on bowtie2 alignment to the vog217 database. TableS9: Top 5 hits of PAU phage on 4 virus databases (GVD, GPD, MGV and IMG_VR4.1). TableS10: Characteristics of phage genomes included in the mock communities from the present study, as well as growth conditions for the strains in the mock communities. TableS11: Average alignment rate of each library to the customed databases for all the mock communities tested in the present study.