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t5 2 caption a7 species strain mic  (ATCC)


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    ATCC t5 2 caption a7 species strain mic
    T5 2 Caption A7 Species Strain Mic, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 2840 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    KEY RESOURCES TABLE

    Journal: Cell systems

    Article Title: Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

    doi: 10.1016/j.cels.2021.08.009

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: Although rust-mdbg metagenome assemblies are consistently more fragmented than hifiasm-meta assemblies, the ability of rust-mdbg to very quickly assemble a metagenome enables instant quality control and preliminary exploration of gene content of microbiomes at a fraction of the computing costs of current tools. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Zymo D6331 Species Abundance hifiasm rust-mdbg ATCC MSA-1003 Species Abundance hifiasm rust-mdbg A. muciniphila 1.36% 100.00% 100.00% A. baumannii 0.18% 99.84% 99.96% B. fragilis 13.13% 99.99% 100.00% B. pacificus 1.80% 100.00% 100.00% B. adolescentis 1.34% 100.00% 99.73% B. vulgatus 0.02% 81.85% 70.90% C. albicans 1.61% 67.83% 39.82% B. adolescentis 0.02% 5.24% 0.64% C. difficile 1.83% 100.00% 99.98% C. beijerinckii 1.80% 99.99% 99.99% C. perfringens 0.00% 0.01% 0.01% C. acnes 0.18% 100.00% 100.00% E. faecalis 0.00% 0.01% 0.01% D. radiodurans 0.02% 82.50% 53.66% E. coli B1109 8.44% 100.00% 97.92% E. faecalis 0.02% 54.98% 21.05% E. coli b2207 8.32% 100.00% 98.66% E. coli 18.00% 100.00% 100.00% E. coli B3008 8.25% 100.00% 99.56% H. pylori 0.18% 100.00% 100.00% E. coli B766 7.83% 96.91% 96.27% L. gasseri 0.18% 97.78% 98.14% E. coli JM109 8.37% 100.00% 97.85% N. meningitidis 0.18% 98.59% 99.03% F. prausnitzii 14.39% 100.00% 100.00% P. gingivalis 18.00% 91.74% 99.94% F. nucleatum 3.78% 100.00% 99.96% P. aeruginosa 1.80% 99.71% 99.73% L. fermentum 0.86% 100.00% 100.00% R. sphaeroides 18.00% 99.75% 100.00% M. smithii 0.04% 99.84% 87.18% S. odontolytica 0.02% 8.18% 1.05% P. corporis 5.37% 99.56% 99.56% S. aureus 1.80% 100.00% 100.00% R. hominis 3.88% 100.00% 100.00% S. epidermidis 18.00% 100.00% 100.00% S. cerevisiae 0.18% 69.52% 39.56% S. agalactiae 1.80% 99.50% 99.98% S. enterica 0.02% 6.23% 4.62% S. mutans 18.00% 100.00% 100.00% V. rogosae 11.02% 100.00% 100.00% – – – – Running time – 34 h 29 min 55s – – 59 h 16 min 3 min 51 s Memory usage – 83 GB 0.9 GB – – 313 GB 1.3 GB Open in a separate window The Abundance column shows the relative abundance of the species in the sample.

    Techniques: Software

    Metagenome assembly statistics of the Zymo D6331 dataset (left) and the ATCC MSA-1003 dataset (right) using hifiasm-meta and rust-mdbg

    Journal: Cell systems

    Article Title: Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

    doi: 10.1016/j.cels.2021.08.009

    Figure Lengend Snippet: Metagenome assembly statistics of the Zymo D6331 dataset (left) and the ATCC MSA-1003 dataset (right) using hifiasm-meta and rust-mdbg

    Article Snippet: Although rust-mdbg metagenome assemblies are consistently more fragmented than hifiasm-meta assemblies, the ability of rust-mdbg to very quickly assemble a metagenome enables instant quality control and preliminary exploration of gene content of microbiomes at a fraction of the computing costs of current tools. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Zymo D6331 Species Abundance hifiasm rust-mdbg ATCC MSA-1003 Species Abundance hifiasm rust-mdbg A. muciniphila 1.36% 100.00% 100.00% A. baumannii 0.18% 99.84% 99.96% B. fragilis 13.13% 99.99% 100.00% B. pacificus 1.80% 100.00% 100.00% B. adolescentis 1.34% 100.00% 99.73% B. vulgatus 0.02% 81.85% 70.90% C. albicans 1.61% 67.83% 39.82% B. adolescentis 0.02% 5.24% 0.64% C. difficile 1.83% 100.00% 99.98% C. beijerinckii 1.80% 99.99% 99.99% C. perfringens 0.00% 0.01% 0.01% C. acnes 0.18% 100.00% 100.00% E. faecalis 0.00% 0.01% 0.01% D. radiodurans 0.02% 82.50% 53.66% E. coli B1109 8.44% 100.00% 97.92% E. faecalis 0.02% 54.98% 21.05% E. coli b2207 8.32% 100.00% 98.66% E. coli 18.00% 100.00% 100.00% E. coli B3008 8.25% 100.00% 99.56% H. pylori 0.18% 100.00% 100.00% E. coli B766 7.83% 96.91% 96.27% L. gasseri 0.18% 97.78% 98.14% E. coli JM109 8.37% 100.00% 97.85% N. meningitidis 0.18% 98.59% 99.03% F. prausnitzii 14.39% 100.00% 100.00% P. gingivalis 18.00% 91.74% 99.94% F. nucleatum 3.78% 100.00% 99.96% P. aeruginosa 1.80% 99.71% 99.73% L. fermentum 0.86% 100.00% 100.00% R. sphaeroides 18.00% 99.75% 100.00% M. smithii 0.04% 99.84% 87.18% S. odontolytica 0.02% 8.18% 1.05% P. corporis 5.37% 99.56% 99.56% S. aureus 1.80% 100.00% 100.00% R. hominis 3.88% 100.00% 100.00% S. epidermidis 18.00% 100.00% 100.00% S. cerevisiae 0.18% 69.52% 39.56% S. agalactiae 1.80% 99.50% 99.98% S. enterica 0.02% 6.23% 4.62% S. mutans 18.00% 100.00% 100.00% V. rogosae 11.02% 100.00% 100.00% – – – – Running time – 34 h 29 min 55s – – 59 h 16 min 3 min 51 s Memory usage – 83 GB 0.9 GB – – 313 GB 1.3 GB Open in a separate window The Abundance column shows the relative abundance of the species in the sample.

    Techniques:

    KEY RESOURCES TABLE

    Journal: Cell systems

    Article Title: Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

    doi: 10.1016/j.cels.2021.08.009

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: Although rust-mdbg metagenome assemblies are consistently more fragmented than hifiasm-meta assemblies, the ability of rust-mdbg to very quickly assemble a metagenome enables instant quality control and preliminary exploration of gene content of microbiomes at a fraction of the computing costs of current tools. table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Zymo D6331 Species Abundance hifiasm rust-mdbg ATCC MSA-1003 Species Abundance hifiasm rust-mdbg A. muciniphila 1.36% 100.00% 100.00% A. baumannii 0.18% 99.84% 99.96% B. fragilis 13.13% 99.99% 100.00% B. pacificus 1.80% 100.00% 100.00% B. adolescentis 1.34% 100.00% 99.73% B. vulgatus 0.02% 81.85% 70.90% C. albicans 1.61% 67.83% 39.82% B. adolescentis 0.02% 5.24% 0.64% C. difficile 1.83% 100.00% 99.98% C. beijerinckii 1.80% 99.99% 99.99% C. perfringens 0.00% 0.01% 0.01% C. acnes 0.18% 100.00% 100.00% E. faecalis 0.00% 0.01% 0.01% D. radiodurans 0.02% 82.50% 53.66% E. coli B1109 8.44% 100.00% 97.92% E. faecalis 0.02% 54.98% 21.05% E. coli b2207 8.32% 100.00% 98.66% E. coli 18.00% 100.00% 100.00% E. coli B3008 8.25% 100.00% 99.56% H. pylori 0.18% 100.00% 100.00% E. coli B766 7.83% 96.91% 96.27% L. gasseri 0.18% 97.78% 98.14% E. coli JM109 8.37% 100.00% 97.85% N. meningitidis 0.18% 98.59% 99.03% F. prausnitzii 14.39% 100.00% 100.00% P. gingivalis 18.00% 91.74% 99.94% F. nucleatum 3.78% 100.00% 99.96% P. aeruginosa 1.80% 99.71% 99.73% L. fermentum 0.86% 100.00% 100.00% R. sphaeroides 18.00% 99.75% 100.00% M. smithii 0.04% 99.84% 87.18% S. odontolytica 0.02% 8.18% 1.05% P. corporis 5.37% 99.56% 99.56% S. aureus 1.80% 100.00% 100.00% R. hominis 3.88% 100.00% 100.00% S. epidermidis 18.00% 100.00% 100.00% S. cerevisiae 0.18% 69.52% 39.56% S. agalactiae 1.80% 99.50% 99.98% S. enterica 0.02% 6.23% 4.62% S. mutans 18.00% 100.00% 100.00% V. rogosae 11.02% 100.00% 100.00% – – – – Running time – 34 h 29 min 55s – – 59 h 16 min 3 min 51 s Memory usage – 83 GB 0.9 GB – – 313 GB 1.3 GB Open in a separate window The Abundance column shows the relative abundance of the species in the sample.

    Techniques: Software

    Summary of in silico taxonomic findings for the 14 representative genomospecies from Fig. 1 . a

    Journal: Clinical Chemistry

    Article Title: In Silico Analysis of Gardnerella Genomospecies Detected in the Setting of Bacterial Vaginosis

    doi: 10.1373/clinchem.2019.305474

    Figure Lengend Snippet: Summary of in silico taxonomic findings for the 14 representative genomospecies from Fig. 1 . a

    Article Snippet: The AAI calculator was the only tool that considered GED7760B the same genomospecies as G. piotii UGENT 18.01 (T)/JCP8017A. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Number Species/strain Assembly Method Jspecies-ANIb Jspecies-Tetra Kostas-ANI Kostas-AAI Conservative consensus 01 G. vaginalis ATCC 14018 (T) GCA_000178355.1 01 01 = 02 01 01 = 02 GS01 (01 = 02) 02 JCP8108 GCA_000414525.1 02 02 03 JCP8017A GCA_000414605.1 03 03 = 04 03 03 = 04 = 11 GS02 (03 = 04) 04 G. piotii UGENT 18.01 (T) GCA_003397585.1 04 04 05 G. leopoldii UGENT 06.41 (T) GCA_003293675.1 05 05 = 06 05 = 06 05 = 06 GS03 (05 = 06) 06 G. swidsinkii 9838–1 (T) GCA_003397705.1 06 07 JCP8481A GCA_000414465.1 07 07 07 07 GS04 (07) 08 UMB1686 GCA_002884775.1 08 08 = 09 = 10 08 08 = 09 = 10 GS05 (08 = 09 = 10) 09 6119V5 GCA_000263655.1 09 09 = 10 10 1500E GCA_000263595.1 10 11 GED7760B GCA_001546455.1 11 11 11 GS06 (11) 12 CMW7778B GCA_001563665.1 12 12 12 12 GS07 (12) 13 KA00225 GCA_002896555.1 13 13 13 13 GS08 (13) 14 NR010 GCA_003408845.1 14 14 14 14 GS09 (14) Number of species 14 9 12 8 9 Open in a separate window a The number corresponds to the depiction in .

    Techniques: In Silico