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CosmosID Inc bioinformatics software package
Bioinformatics Software Package, supplied by CosmosID Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bioinformatics+software+package/bioinformatics+software+package/pm40595471-213-13-17
Average 90 stars, based on 1 article reviews
bioinformatics software package - by Bioz Stars, 2026-10
90/100 stars

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Related Articles

Sequencing:

Article Title: Carbapenemase-producing Enterobacterales and their carbapenemase genes are stably recovered across the wastewater-watershed ecosystem nexus.
Article Snippet: Shotgun sequencing was performed using the HiSeq 2000 system (Illumina). .. Unassembled metagenomic sequencing reads were directly analyzed using the CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD) as previously described (Hasan et al., 2014; Ottesen et al., 2016; Ponnusamy et al., 2016) to achieve identification at the species, subspecies, and/or strain levels and quantification of organism's relative abundance. .. Antibiotic resistance genes (ARGs) in the microbiome were profiled by querying unassembled sequence reads against CosmosID curated antibiotic resistance databases (Chekabab et al., 2020; Yan et al., 2019).

Article Title: Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin
Article Snippet: All sequencing was done using 2 × 150 bp using Illumina HiSeq 4000 Instrument (Illumina Inc., San Diego, CA, USA). .. Unassembled metagenomic sequencing reads from the dataset and HMP westerners were analyzed using CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States), as described previously in ref. . Human reads were removed using genome assembly GRCh38_p6 and normalized by subsampling to 13 M reads using reformat.sh of the BBTools suite ( http://bbtools.jgi.doe.gov ). .. Processed reads were classified to taxa using CosmosID portal, employing k-mer mapping to unique genome regions for each taxon , (details in Supplementary Methods).

Article Title: Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources
Article Snippet: The libraries were pooled by adding an equimolar ratio of each based on the concentration determined by PicoGreen, and loaded onto a high sensitivity (HS) chip run on the Caliper LabChipGX (Perkin Elmer, Waltham, MA, USA) for size estimation, followed by 150 bp paired end sequencing using Illumina HiSeq v3 chemistry (Illumina, San Diego, CA, USA). .. Sequencing reads were directly analyzed using the CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States) as described previously [ , , , ]. ..

Article Title: Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.
Article Snippet: All sequencing was done using 2 × 150bp using Illumina HiSeq 4000 Instrument (Illumina Inc., San Diego, CA, USA). .. Unassembled metagenomic sequencing reads from the dataset and HMP westerners were analyzed using CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States), as described previously in ref.70. .. Human reads were removed using genome assembly GRCh38_p6 and normalized by subsampling to 13M reads using reformat.sh of the BBTools suite (http://bbtools.jgi.doe. gov).

Article Title: Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin
Article Snippet: All sequencing was done using 2 x 150bp using Illumina HiSeq 4000 Instrument (Illumina Inc., San Diego, CA, USA). .. Unassembled metagenomic sequencing reads from the dataset and HMP westerners were analyzed using CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States), as described previously . .. Human reads were removed using genome assembly GRCh38_p6 and normalized by subsampling to 13M reads using reformat.sh of the BBTools suite ( http://bbtools.jgi.doe.gov ).

Software:

Article Title: Carbapenemase-producing Enterobacterales and their carbapenemase genes are stably recovered across the wastewater-watershed ecosystem nexus.
Article Snippet: Shotgun sequencing was performed using the HiSeq 2000 system (Illumina). .. Unassembled metagenomic sequencing reads were directly analyzed using the CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD) as previously described (Hasan et al., 2014; Ottesen et al., 2016; Ponnusamy et al., 2016) to achieve identification at the species, subspecies, and/or strain levels and quantification of organism's relative abundance. .. Antibiotic resistance genes (ARGs) in the microbiome were profiled by querying unassembled sequence reads against CosmosID curated antibiotic resistance databases (Chekabab et al., 2020; Yan et al., 2019).

Article Title: Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin
Article Snippet: All sequencing was done using 2 × 150 bp using Illumina HiSeq 4000 Instrument (Illumina Inc., San Diego, CA, USA). .. Unassembled metagenomic sequencing reads from the dataset and HMP westerners were analyzed using CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States), as described previously in ref. . Human reads were removed using genome assembly GRCh38_p6 and normalized by subsampling to 13 M reads using reformat.sh of the BBTools suite ( http://bbtools.jgi.doe.gov ). .. Processed reads were classified to taxa using CosmosID portal, employing k-mer mapping to unique genome regions for each taxon , (details in Supplementary Methods).

Article Title: Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources
Article Snippet: The libraries were pooled by adding an equimolar ratio of each based on the concentration determined by PicoGreen, and loaded onto a high sensitivity (HS) chip run on the Caliper LabChipGX (Perkin Elmer, Waltham, MA, USA) for size estimation, followed by 150 bp paired end sequencing using Illumina HiSeq v3 chemistry (Illumina, San Diego, CA, USA). .. Sequencing reads were directly analyzed using the CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States) as described previously [ , , , ]. ..

Article Title: A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes
Article Snippet: Raw datasets Fastq files were analysed using the CosmosID software to identify bacteria, protists, bacteriophages, viruses, fungi, virulence factor genes and antibiotic resistance genes. .. The CosmosID bioinformatics software package utilises a high-performance data-mining K-mer based algorithm that disambiguates hundreds of millions of short reads of a metagenomic sample into the discrete microorganisms engendering the particular sequences. ..

Article Title: The role of mobile phones as a possible pathway for pathogen movement, a cross-sectional microbial analysis.
Article Snippet: Following the sequencing runs, data provided as demultiplexed FASTQ files were uploaded into CosmosID (https://www.cosmosid.com /) software to identify bacteria, VFGs and ARGs. .. The CosmosID bioinformatics software package utilises a high-performance data-mining Kmer based algorithm that disambiguates hundreds of millions of short reads of a metagenomic sample into the discrete microorganisms engendering the particular sequences. ..

Article Title: Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.
Article Snippet: All sequencing was done using 2 × 150bp using Illumina HiSeq 4000 Instrument (Illumina Inc., San Diego, CA, USA). .. Unassembled metagenomic sequencing reads from the dataset and HMP westerners were analyzed using CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States), as described previously in ref.70. .. Human reads were removed using genome assembly GRCh38_p6 and normalized by subsampling to 13M reads using reformat.sh of the BBTools suite (http://bbtools.jgi.doe. gov).

Article Title: Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin
Article Snippet: All sequencing was done using 2 x 150bp using Illumina HiSeq 4000 Instrument (Illumina Inc., San Diego, CA, USA). .. Unassembled metagenomic sequencing reads from the dataset and HMP westerners were analyzed using CosmosID bioinformatics software package (CosmosID Inc., Rockville, MD, United States), as described previously . .. Human reads were removed using genome assembly GRCh38_p6 and normalized by subsampling to 13M reads using reformat.sh of the BBTools suite ( http://bbtools.jgi.doe.gov ).

other:

Article Title: Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds
Article Snippet: Sequencing reads were analyzed for identification of microbial DNA at the species level 90 and determination of the organism’s relative abundance using the CosmosID bioinformatics 91 software package (CosmosID Inc., Rockville, MD).



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