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ncbi file transfer protocol (ftp) genomes repository of refseq representative assemblies  (Biotechnology Information)

 
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    Biotechnology Information ncbi file transfer protocol (ftp) genomes repository of refseq representative assemblies
    General alignment statistics (including read counts) are reported at the start of the report for all defined pathogens and commensals (disabled by default; displayed in lower table). Those marked with a star denote high-consequence pathogens, including those on the NIAID biodefense pathogen list . Organisms without class labels (i.e., not categorized/classified as pathogenic or commensal) are reported in the supplementary Unannotated Organisms list. This example report was generated from multiple in silico data samples, generated with various depth of coverage profiles using InSilicoSeq and references were curated from NCBI’s <t>Refseq</t> database . Additional annotation explanations are available later in the report (not depicted in the sample figure). Supplemental or intermediate files are available in output directories according to their function within the workflow and can be used according to additional bioinformatics downstream requirements if needed.
    Ncbi File Transfer Protocol (Ftp) Genomes Repository Of Refseq Representative Assemblies, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection"

    Article Title: TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection

    Journal: bioRxiv

    doi: 10.1101/2025.07.16.664785

    General alignment statistics (including read counts) are reported at the start of the report for all defined pathogens and commensals (disabled by default; displayed in lower table). Those marked with a star denote high-consequence pathogens, including those on the NIAID biodefense pathogen list . Organisms without class labels (i.e., not categorized/classified as pathogenic or commensal) are reported in the supplementary Unannotated Organisms list. This example report was generated from multiple in silico data samples, generated with various depth of coverage profiles using InSilicoSeq and references were curated from NCBI’s Refseq database . Additional annotation explanations are available later in the report (not depicted in the sample figure). Supplemental or intermediate files are available in output directories according to their function within the workflow and can be used according to additional bioinformatics downstream requirements if needed.
    Figure Legend Snippet: General alignment statistics (including read counts) are reported at the start of the report for all defined pathogens and commensals (disabled by default; displayed in lower table). Those marked with a star denote high-consequence pathogens, including those on the NIAID biodefense pathogen list . Organisms without class labels (i.e., not categorized/classified as pathogenic or commensal) are reported in the supplementary Unannotated Organisms list. This example report was generated from multiple in silico data samples, generated with various depth of coverage profiles using InSilicoSeq and references were curated from NCBI’s Refseq database . Additional annotation explanations are available later in the report (not depicted in the sample figure). Supplemental or intermediate files are available in output directories according to their function within the workflow and can be used according to additional bioinformatics downstream requirements if needed.

    Techniques Used: Generated, In Silico



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    ncbi file transfer protocol (ftp) genomes repository of refseq representative assemblies  (Biotechnology Information)
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    Divergence times of multiple falcon species and populations. ( A) Bayesian chronogram (time-calibrated phylogenetic tree) of 42 falcons based on whole mitogenome (mtDNA) sequences (excluding the control region, CR) with chicken mtDNA as an outgroup, generated using Beast2. The nodes are labeled with divergence time in million years ago (MYA), based on the estimated divergence time between chicken and falcons of 88 ± 10 MYA. A full tree with confidence intervals of the age estimates can be found in Fig. S3. ( B) Maximum-likelihood phylogenetic tree using an alignment of W-specific variants (3,007 SNPs) in 39 female falcons. The tree was constructed using K2P + R2, which was the best-fit model according to BIC. Branch labels represent SH-aLRT support (%), aBayes support, and ultrafast bootstrap support (%), respectively. The red cluster denotes gyrfalcons (GF) and the green denotes Altai gyrfalcon-like falcons (GLF), the blue cluster represents sakers (SF), and the purple cluster represents saker-like Altai falcons (SLF). SP19 mitogenome is the reference mitogenome that was assembled in this project. Gray labels refer to hybrid individuals that were added to validate the W chromosome haplotype results. Sequences (labeled with the species name) were retrieved from <t>NCBI</t> (Accession numbers: common kestrel NC_011307.1, American kestrel NC_008547.1, merlin KM264304.1, saker NC_026715.1, peregrine 1 NC_000878.1, peregrine 2 JQ282801.1 and gyrfalcon KT989235.1).
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    Maximum-likelihood phylogenetic tree of the 52 clinical Aeromonas isolates from this study as well as seven representative Aeromonas reference strains and three reference strains of the genus Tolumonas from <t>NCBI</t> generated by using Panaroo v1.3.4 and IQ-TREE v2.2.0. The tree was visualized in iTOL v6 and rooted on the Tolumonas outgroup. Branch support values (SH-aLRT) were calculated in 1,000 replicates and are indicated as triangles on the branches. The size of the triangle correlates with the support value. The scale bar represents the average number of substitutions per site.
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    Image Search Results


    General alignment statistics (including read counts) are reported at the start of the report for all defined pathogens and commensals (disabled by default; displayed in lower table). Those marked with a star denote high-consequence pathogens, including those on the NIAID biodefense pathogen list . Organisms without class labels (i.e., not categorized/classified as pathogenic or commensal) are reported in the supplementary Unannotated Organisms list. This example report was generated from multiple in silico data samples, generated with various depth of coverage profiles using InSilicoSeq and references were curated from NCBI’s Refseq database . Additional annotation explanations are available later in the report (not depicted in the sample figure). Supplemental or intermediate files are available in output directories according to their function within the workflow and can be used according to additional bioinformatics downstream requirements if needed.

    Journal: bioRxiv

    Article Title: TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection

    doi: 10.1101/2025.07.16.664785

    Figure Lengend Snippet: General alignment statistics (including read counts) are reported at the start of the report for all defined pathogens and commensals (disabled by default; displayed in lower table). Those marked with a star denote high-consequence pathogens, including those on the NIAID biodefense pathogen list . Organisms without class labels (i.e., not categorized/classified as pathogenic or commensal) are reported in the supplementary Unannotated Organisms list. This example report was generated from multiple in silico data samples, generated with various depth of coverage profiles using InSilicoSeq and references were curated from NCBI’s Refseq database . Additional annotation explanations are available later in the report (not depicted in the sample figure). Supplemental or intermediate files are available in output directories according to their function within the workflow and can be used according to additional bioinformatics downstream requirements if needed.

    Article Snippet: In TaxTriage with access to the external internet, the default pipeline uses the classification output to identify the species to be downloaded from the National Center for Biotechnology Information (NCBI) file transfer protocol (FTP) genomes repository of RefSeq representative assemblies.

    Techniques: Generated, In Silico

    Divergence times of multiple falcon species and populations. ( A) Bayesian chronogram (time-calibrated phylogenetic tree) of 42 falcons based on whole mitogenome (mtDNA) sequences (excluding the control region, CR) with chicken mtDNA as an outgroup, generated using Beast2. The nodes are labeled with divergence time in million years ago (MYA), based on the estimated divergence time between chicken and falcons of 88 ± 10 MYA. A full tree with confidence intervals of the age estimates can be found in Fig. S3. ( B) Maximum-likelihood phylogenetic tree using an alignment of W-specific variants (3,007 SNPs) in 39 female falcons. The tree was constructed using K2P + R2, which was the best-fit model according to BIC. Branch labels represent SH-aLRT support (%), aBayes support, and ultrafast bootstrap support (%), respectively. The red cluster denotes gyrfalcons (GF) and the green denotes Altai gyrfalcon-like falcons (GLF), the blue cluster represents sakers (SF), and the purple cluster represents saker-like Altai falcons (SLF). SP19 mitogenome is the reference mitogenome that was assembled in this project. Gray labels refer to hybrid individuals that were added to validate the W chromosome haplotype results. Sequences (labeled with the species name) were retrieved from NCBI (Accession numbers: common kestrel NC_011307.1, American kestrel NC_008547.1, merlin KM264304.1, saker NC_026715.1, peregrine 1 NC_000878.1, peregrine 2 JQ282801.1 and gyrfalcon KT989235.1).

    Journal: Scientific Reports

    Article Title: Chromosome-level reference genome assembly of the gyrfalcon ( Falco rusticolus ) and population genomics offer insights into the falcon population in Mongolia

    doi: 10.1038/s41598-025-88216-9

    Figure Lengend Snippet: Divergence times of multiple falcon species and populations. ( A) Bayesian chronogram (time-calibrated phylogenetic tree) of 42 falcons based on whole mitogenome (mtDNA) sequences (excluding the control region, CR) with chicken mtDNA as an outgroup, generated using Beast2. The nodes are labeled with divergence time in million years ago (MYA), based on the estimated divergence time between chicken and falcons of 88 ± 10 MYA. A full tree with confidence intervals of the age estimates can be found in Fig. S3. ( B) Maximum-likelihood phylogenetic tree using an alignment of W-specific variants (3,007 SNPs) in 39 female falcons. The tree was constructed using K2P + R2, which was the best-fit model according to BIC. Branch labels represent SH-aLRT support (%), aBayes support, and ultrafast bootstrap support (%), respectively. The red cluster denotes gyrfalcons (GF) and the green denotes Altai gyrfalcon-like falcons (GLF), the blue cluster represents sakers (SF), and the purple cluster represents saker-like Altai falcons (SLF). SP19 mitogenome is the reference mitogenome that was assembled in this project. Gray labels refer to hybrid individuals that were added to validate the W chromosome haplotype results. Sequences (labeled with the species name) were retrieved from NCBI (Accession numbers: common kestrel NC_011307.1, American kestrel NC_008547.1, merlin KM264304.1, saker NC_026715.1, peregrine 1 NC_000878.1, peregrine 2 JQ282801.1 and gyrfalcon KT989235.1).

    Article Snippet: The final annotation of the assembly was done using the National Center for Biotechnology Information (NCBI) Eukaryotic Genome Annotation Pipeline, with the assembly upgraded to NCBI RefSeq assembly (GCF_015220075.1).

    Techniques: Control, Generated, Labeling, Construct

    Maximum-likelihood phylogenetic tree of the 52 clinical Aeromonas isolates from this study as well as seven representative Aeromonas reference strains and three reference strains of the genus Tolumonas from NCBI generated by using Panaroo v1.3.4 and IQ-TREE v2.2.0. The tree was visualized in iTOL v6 and rooted on the Tolumonas outgroup. Branch support values (SH-aLRT) were calculated in 1,000 replicates and are indicated as triangles on the branches. The size of the triangle correlates with the support value. The scale bar represents the average number of substitutions per site.

    Journal: Frontiers in Microbiology

    Article Title: Emerging Aeromonas spp. infections in Europe: characterization of human clinical isolates from German patients

    doi: 10.3389/fmicb.2024.1498180

    Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of the 52 clinical Aeromonas isolates from this study as well as seven representative Aeromonas reference strains and three reference strains of the genus Tolumonas from NCBI generated by using Panaroo v1.3.4 and IQ-TREE v2.2.0. The tree was visualized in iTOL v6 and rooted on the Tolumonas outgroup. Branch support values (SH-aLRT) were calculated in 1,000 replicates and are indicated as triangles on the branches. The size of the triangle correlates with the support value. The scale bar represents the average number of substitutions per site.

    Article Snippet: NCBI RefSeq/assembly accessions are NZ_CDDA00000000.1/GCF_000819745.1 ( Aeromonas bestiarum CECT 4227 T ), NZ_LS483441.1/GCF_900476005.1 ( Aeromonas caviae NCTC 12244 T ), NZ_CDBH00000000.1/GCF_000820305.1 ( Aeromonas dhakensis CIP 107500 T ), NZ_CDDI00000000.1/GCF_000819825.1 ( Aeromonas encheleia CECT 4342 T ), NC_008570.1/GCF_000014805.1 ( Aeromonas hydrophila ATCC 7966 T ), NZ_CDBZ00000000.1/GCF_000819985.1 ( Aeromonas media CECT 4232 T ), NZ_CP027856.1/GCF_003015165.1 ( Aeromonas rivipollensis KN-Mc-11 N1), NZ_UAPT00000000.1/GCF_900445115.1 ( Aeromonas salmonicida NCTC 12959 T ), NZ_CDDK00000000.1/GCF_000820225.1 ( Aeromonas veronii CECT 4257 T ), NC_012691.1/GCF_000023065.1 ( Tolumonas auensis DSM 9187 T ), NZ_AZUK00000000.1/GCF_000527035.1 ( Tolumonas lignilytica BRL6-1 T ), and NZ_JACHGR000000000.1/GCF_014202415.1 ( Tolumonas osonensis DSM 22975 T ).

    Techniques: Generated

    Maximum-likelihood phylogenetic trees of the three main Aeromonas species from this study generated using the snippySnake pipeline v1.3.0 in combination with IQ-TREE v2.2.0, visualized in iTOL v6 and manually rooted to the respective NCBI reference genome. (A) Aeromonas caviae phylogenetic tree based on 217,564 SNP positions. (B) Aeromonas hydrophila phylogenetic tree based on 316,836 SNP positions. (C) Aeromonas veronii phylogenetic tree based on 395,268 SNP positions. Branch support values (SH-aLRT) were calculated in 1,000 replicates and are indicated as triangles on the branches. The size of the triangle correlates with the support value. The scale bar represents the average number of substitutions per SNP position.

    Journal: Frontiers in Microbiology

    Article Title: Emerging Aeromonas spp. infections in Europe: characterization of human clinical isolates from German patients

    doi: 10.3389/fmicb.2024.1498180

    Figure Lengend Snippet: Maximum-likelihood phylogenetic trees of the three main Aeromonas species from this study generated using the snippySnake pipeline v1.3.0 in combination with IQ-TREE v2.2.0, visualized in iTOL v6 and manually rooted to the respective NCBI reference genome. (A) Aeromonas caviae phylogenetic tree based on 217,564 SNP positions. (B) Aeromonas hydrophila phylogenetic tree based on 316,836 SNP positions. (C) Aeromonas veronii phylogenetic tree based on 395,268 SNP positions. Branch support values (SH-aLRT) were calculated in 1,000 replicates and are indicated as triangles on the branches. The size of the triangle correlates with the support value. The scale bar represents the average number of substitutions per SNP position.

    Article Snippet: NCBI RefSeq/assembly accessions are NZ_CDDA00000000.1/GCF_000819745.1 ( Aeromonas bestiarum CECT 4227 T ), NZ_LS483441.1/GCF_900476005.1 ( Aeromonas caviae NCTC 12244 T ), NZ_CDBH00000000.1/GCF_000820305.1 ( Aeromonas dhakensis CIP 107500 T ), NZ_CDDI00000000.1/GCF_000819825.1 ( Aeromonas encheleia CECT 4342 T ), NC_008570.1/GCF_000014805.1 ( Aeromonas hydrophila ATCC 7966 T ), NZ_CDBZ00000000.1/GCF_000819985.1 ( Aeromonas media CECT 4232 T ), NZ_CP027856.1/GCF_003015165.1 ( Aeromonas rivipollensis KN-Mc-11 N1), NZ_UAPT00000000.1/GCF_900445115.1 ( Aeromonas salmonicida NCTC 12959 T ), NZ_CDDK00000000.1/GCF_000820225.1 ( Aeromonas veronii CECT 4257 T ), NC_012691.1/GCF_000023065.1 ( Tolumonas auensis DSM 9187 T ), NZ_AZUK00000000.1/GCF_000527035.1 ( Tolumonas lignilytica BRL6-1 T ), and NZ_JACHGR000000000.1/GCF_014202415.1 ( Tolumonas osonensis DSM 22975 T ).

    Techniques: Generated

    Distribution of papA variants among papC + E. coli genomes from NCBI Assembly Refseq database.

    Journal: International Journal of Molecular Sciences

    Article Title: Distribution of papA and papG Variants among Escherichia coli Genotypes: Association with Major Extraintestinal Pathogenic Lineages

    doi: 10.3390/ijms25126657

    Figure Lengend Snippet: Distribution of papA variants among papC + E. coli genomes from NCBI Assembly Refseq database.

    Article Snippet: Screening of pap genes : A total of 35.828 E. coli genomes were obtained from the Assembly Refseq database available in the National Center for Biotechnology Information (NCBI) of the United States of America ( https://www.ncbi.nlm.nih.gov/genbank/ , accessed on 8 January 2024) [ ].

    Techniques: Variant Assay, Sequencing

    Distribution of papG variants among papC + E. coli genomes from NCBI Assembly Refseq database.

    Journal: International Journal of Molecular Sciences

    Article Title: Distribution of papA and papG Variants among Escherichia coli Genotypes: Association with Major Extraintestinal Pathogenic Lineages

    doi: 10.3390/ijms25126657

    Figure Lengend Snippet: Distribution of papG variants among papC + E. coli genomes from NCBI Assembly Refseq database.

    Article Snippet: Screening of pap genes : A total of 35.828 E. coli genomes were obtained from the Assembly Refseq database available in the National Center for Biotechnology Information (NCBI) of the United States of America ( https://www.ncbi.nlm.nih.gov/genbank/ , accessed on 8 January 2024) [ ].

    Techniques: Variant Assay, Sequencing