Supplementary material 1 from: Macher J, Macher T, Leese F (2017) Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger. Metabarcoding and Metagenomics 1: e22262. https://doi.org/10.3897/mbmg.1.22262

CRUX: Creating Reference libraries Using eXisting tools

Curd, Emily
Kandlikar, Gaurav
Gomer, Jesse

May 2019

Taxonomic assignments of metabarcoding reads requires a comprehensive reference library. There are p...

Supplementary material 6 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}

Buchner, Dominik
Haase, Peter
Leese, Florian

July 2021

Figure S1. Pictures were taken with a digital microscope (Keyence VHX-6000, Keyence, Osaka, Japan

Metabarcode_OTUtables

Ransome, Emma
Geller, Jonathan B.
Timmers, Molly
Leray, Matthieu
Mahardini, Angka
Sembiring, Andrianus
Collins, Allen G.
Meyer, Christopher P.

April 2017

This file contains an OTU table from each experiment and identifications for each OTU from Biocode, ...

Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger

Macher, Jan-Niklas
Macher, Till-Hendrik
Leese, Florian

December 2017

Metabarcoding and metagenomic approaches are becoming routine techniquesfor use in biodiversity asse...

Metabarcode_OTU_table

Matthieu Leray (170606)
Nancy Knowlton (41636)

October 2016

The column "source ID" presents how each OTU was identified. SAP: Statistical assignment Package; NC...

Supplementary material 7 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}

Buchner, Dominik
Haase, Peter
Leese, Florian

July 2021

Figure S2. Baseline-corrected amplification curves (left half) and melting -curves (right half) for ...

1 MetaABC – an integrated Metagenomics platform for data Ad- justment, Binning, and Clustering

Chien-hao Su
Ming-tsung Hsu
Tse-yi Wang
Su-feng Chiang
Jen-hao Cheng
Francis C Weng
Cheng-yan Kao
Daryi Wang
Huai-kuang Tsai

October 2016

Summary: MetaABC is a metagenomic platform that integrates several binning tools coupled with method...

Supplementary Files: Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC)

Jessica L.S. Zylla*
Mariah M. Hoffman*
Somshuvra Bhattacharya
Kristin Calar
Yohannes Afeworki
Pilar de la Puente
Etienne Z. Gnimpieba
W. Keith Miskimins
Shanta M. Messerli

January 2022

*denotes Co-First Authorship SuppFile1_MethodsandFigures.docx: Supplementary File 1 Methods and Fig...

Supplementary material 1 from: Holovachov O (2016) Metabarcoding of marine nematodes – evaluation of similarity scores used in alignment-based taxonomy assignment approach. Biodiversity Data Journal 4: e10647. https://doi.org/10.3897/BDJ.4.e10647

Holovachov, Oleksandr

November 2016

Table S1. GenBank accession numbers and classification of sequences used in present analysis

Supplementary material 2 from: Vamos E, Elbrecht V, Leese F (2017) Short COI markers for freshwater macroinvertebrate metabarcoding. Metabarcoding and Metagenomics 1: e14625. https://doi.org/10.3897/mbmg.1.14625

Vamos, Ecaterina
Elbrecht, Vasco
Leese, Florian

January 2018

Developed fusion primers for fwh1 and fwh2 on the Illumina high throughput sequencing platform

Jordan_Metabarcode_OTUtable

Al-Rshaidat, Mamoon M. D.
Snider, Allison
Rosebraugh, Sydney
Devine, Amanda M.
Devine, Thomas D.
Plaisance, Laetitia
Knowlton, Nancy
Leray, Matthieu

July 2016

This table summarize the number of sequences per Operational Taxonomic Units (OTU) and per sample. O...

Additional file 1: of DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs

Hirokazu Toju (316083)
Yuki Baba (4042502)

February 2018

Data S1. Keywords used in the downloading of ITS sequences in the NCBI database. (TXT 1Â kb

Additional file 1 of A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads

Vinh Le (3463559)
Lang Tran (737837)
Hoai Tran (3481994)

January 2016

This file contains the NCBI taxonomy versions used in the experiments, the experimental results to v...

Supplementary Figures, Files and Datasets: Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC)

Jessica L.S. Zylla*
Mariah M. Hoffman*
Simona Plesselova
Somshuvra Bhattacharya
Kristin Calar
Yohannes Afeworki
Pilar de la Puente
Etienne Z. Gnimpieba
W. Keith Miskimins
Shanta M. Messerli

January 2022

*denotes Co-First Authorship SuppFile1_Figures.docx: (Updated) Supplementary File 1 Methods and Fig...

Metabarcoding data

Min Tang (142347)
Chloe J. Hardman (3252519)
Yinqiu Ji (2910512)
Guanliang Meng (3252522)
Shanlin Liu (2851853)
Meihua Tang (3252525)
Shenzhou Yang (3252513)
Ellen D. Moss (3252510)
Jiaxin Wang (483624)
Chenxue Yang (3199719)
Catharine Bruce (384651)
Tim Nevard (3252516)
Simon G. Potts (195808)
Xin Zhou (54275)
Douglas W. Yu (211139)

October 2016

This dataset includes the post-denoising (BLUE) and post-merging (FLASH) sequence data, the map file...

CRUX: Creating Reference libraries Using eXisting tools

Curd, Emily
Kandlikar, Gaurav
Gomer, Jesse

May 2019

Taxonomic assignments of metabarcoding reads requires a comprehensive reference library. There are p...

Supplementary material 6 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}

Buchner, Dominik
Haase, Peter
Leese, Florian

July 2021

Figure S1. Pictures were taken with a digital microscope (Keyence VHX-6000, Keyence, Osaka, Japan

Metabarcode_OTUtables

Ransome, Emma
Geller, Jonathan B.
Timmers, Molly
Leray, Matthieu
Mahardini, Angka
Sembiring, Andrianus
Collins, Allen G.
Meyer, Christopher P.

April 2017

This file contains an OTU table from each experiment and identifications for each OTU from Biocode, ...

Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger

Macher, Jan-Niklas
Macher, Till-Hendrik
Leese, Florian

December 2017

Metabarcoding and metagenomic approaches are becoming routine techniquesfor use in biodiversity asse...

Metabarcode_OTU_table

Matthieu Leray (170606)
Nancy Knowlton (41636)

October 2016

The column "source ID" presents how each OTU was identified. SAP: Statistical assignment Package; NC...

Supplementary material 7 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}

Buchner, Dominik
Haase, Peter
Leese, Florian

July 2021

Figure S2. Baseline-corrected amplification curves (left half) and melting -curves (right half) for ...

1 MetaABC – an integrated Metagenomics platform for data Ad- justment, Binning, and Clustering

Chien-hao Su
Ming-tsung Hsu
Tse-yi Wang
Su-feng Chiang
Jen-hao Cheng
Francis C Weng
Cheng-yan Kao
Daryi Wang
Huai-kuang Tsai

October 2016

Summary: MetaABC is a metagenomic platform that integrates several binning tools coupled with method...

Supplementary Files: Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC)

Jessica L.S. Zylla*
Mariah M. Hoffman*
Somshuvra Bhattacharya
Kristin Calar
Yohannes Afeworki
Pilar de la Puente
Etienne Z. Gnimpieba
W. Keith Miskimins
Shanta M. Messerli

January 2022

*denotes Co-First Authorship SuppFile1_MethodsandFigures.docx: Supplementary File 1 Methods and Fig...

Supplementary material 1 from: Holovachov O (2016) Metabarcoding of marine nematodes – evaluation of similarity scores used in alignment-based taxonomy assignment approach. Biodiversity Data Journal 4: e10647. https://doi.org/10.3897/BDJ.4.e10647

Holovachov, Oleksandr

November 2016

Table S1. GenBank accession numbers and classification of sequences used in present analysis

Supplementary material 2 from: Vamos E, Elbrecht V, Leese F (2017) Short COI markers for freshwater macroinvertebrate metabarcoding. Metabarcoding and Metagenomics 1: e14625. https://doi.org/10.3897/mbmg.1.14625

Vamos, Ecaterina
Elbrecht, Vasco
Leese, Florian

January 2018

Developed fusion primers for fwh1 and fwh2 on the Illumina high throughput sequencing platform

Jordan_Metabarcode_OTUtable

Al-Rshaidat, Mamoon M. D.
Snider, Allison
Rosebraugh, Sydney
Devine, Amanda M.
Devine, Thomas D.
Plaisance, Laetitia
Knowlton, Nancy
Leray, Matthieu

July 2016

This table summarize the number of sequences per Operational Taxonomic Units (OTU) and per sample. O...

Additional file 1: of DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs

Hirokazu Toju (316083)
Yuki Baba (4042502)

February 2018

Data S1. Keywords used in the downloading of ITS sequences in the NCBI database. (TXT 1Â kb

Additional file 1 of A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads

Vinh Le (3463559)
Lang Tran (737837)
Hoai Tran (3481994)

January 2016

This file contains the NCBI taxonomy versions used in the experiments, the experimental results to v...

Supplementary Figures, Files and Datasets: Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC)

Jessica L.S. Zylla*
Mariah M. Hoffman*
Simona Plesselova
Somshuvra Bhattacharya
Kristin Calar
Yohannes Afeworki
Pilar de la Puente
Etienne Z. Gnimpieba
W. Keith Miskimins
Shanta M. Messerli

January 2022

*denotes Co-First Authorship SuppFile1_Figures.docx: (Updated) Supplementary File 1 Methods and Fig...

Metabarcoding data

Min Tang (142347)
Chloe J. Hardman (3252519)
Yinqiu Ji (2910512)
Guanliang Meng (3252522)
Shanlin Liu (2851853)
Meihua Tang (3252525)
Shenzhou Yang (3252513)
Ellen D. Moss (3252510)
Jiaxin Wang (483624)
Chenxue Yang (3199719)
Catharine Bruce (384651)
Tim Nevard (3252516)
Simon G. Potts (195808)
Xin Zhou (54275)
Douglas W. Yu (211139)

October 2016

This dataset includes the post-denoising (BLUE) and post-merging (FLASH) sequence data, the map file...

CRUX: Creating Reference libraries Using eXisting tools

Curd, Emily
Kandlikar, Gaurav
Gomer, Jesse

May 2019

Taxonomic assignments of metabarcoding reads requires a comprehensive reference library. There are p...

Supplementary material 6 from: {"en": "Buchner D, Haase P, Leese F (2021) Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics. Metabarcoding and Metagenomics 5: e67533. https://doi.org/10.3897/mbmg.5.67533"}

Buchner, Dominik
Haase, Peter
Leese, Florian

July 2021

Figure S1. Pictures were taken with a digital microscope (Keyence VHX-6000, Keyence, Osaka, Japan

Metabarcode_OTUtables

Ransome, Emma
Geller, Jonathan B.
Timmers, Molly
Leray, Matthieu
Mahardini, Angka
Sembiring, Andrianus
Collins, Allen G.
Meyer, Christopher P.

April 2017

This file contains an OTU table from each experiment and identifications for each OTU from Biocode, ...

Supplementary material 1 from: Macher J, Macher T, Leese F (2017) Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger. Metabarcoding and Metagenomics 1: e22262. https://doi.org/10.3897/mbmg.1.22262

Abstract

Extracted data

Supplementary material 1 from: Macher J, Macher T, Leese F (2017) Combining NCBI and BOLD databases for OTU assignment in metabarcoding and metagenomic datasets: The BOLD_NCBI _Merger. Metabarcoding and Metagenomics 1: e22262. https://doi.org/10.3897/mbmg.1.22262

Abstract

Extracted data

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