Find research datasets worth reusing

TIPP 2.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: TIPP SoftwareVersion: 2.0.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/smirarab/sepp DockerImage: stefanjanssen/docker_profiling_tools:tipp IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: 2015 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:tipp

Bracken 2.5 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: Bracken SoftwareVersion: 2.5 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/jenniferlu717/Bracken DockerImage: cami/bracken:2.5 IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: Kraken standard db built May 2019 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ cami/bracken:2.5

MetaPalette 1.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPalette SoftwareVersion: 1.0.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://doi.org/10.5281/zenodo.1730624 DockerImage: stefanjanssen/docker_profiling_tools:commonkmers IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: https://zenodo.org/record/1749272 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ --volume="/path/to/reference_database:/exchange/db:rw" \ stefanjanssen/docker_profiling_tools:commonkmers

opencc-by-4.0Aug 2022View details →

SPAAM Summer School 2022: Introduction to Ancient Metagenomics - 3c Introduction to Taxonomic Profiling

Teaching data for practical session: "3c Introduction to Taxonomic Profiling" of the 2022 SPAAM Summer School: Introduction to Ancient Metagenomics (Aug. 1-5 2022). See: <a href="https://spaam-community.github.io/wss-summer-school/#/2022/">https://spaam-community.github.io/wss-summer-school/#/2022/</a> or <a href="https://doi.org/10.5281/zenodo.6976711">https://doi.org/10.5281/zenodo.6976711</a> for slides. Once downloaded, run: <pre><code>tar xvfz <session>.tar.gz</code></pre>  to decompress the data directory for the session.

opencc-by-4.0Aug 2024View details →

The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities - Supplementary Tables

Supplementary Table 1: A map between each of the genomes in mOTUs-db (3’747’151), the associated study and its metagenomic sample (in case of MAGs). Columns: <code>    GENOME             → Unique mOTUs-db name of the genome</code> <code>    STUDY              → Unique mOTUs-db name of the study</code> <code>    IS_MAG             → True if genome is a MAG, otherwise False </code> <code>    METAGENOMIC_SAMPLE → Unique name of the metagenomic sample or NA in case of non-MAG genome</code> Example: <code>    GENOME                                     STUDY        IS_MAG    METAGENOMIC_SAMPLE</code> <code>    ---------------------------------------------------------------------------------------------</code> <code>    ACIN21-1_SAMN05421555_MAG_00000001         ACIN21-1     True      ACIN21-1_SAMN05421555_METAG</code> <code>    RSGB23-1_GCA-006096615-V1_GENO_10000001    RSGB23-1     False     NA</code> Supplementary Table 2: A map between all non-MAG genomes (919’090) and their source (e.g. Refseq or JGI). Columns: <code>    GENOME             → Unique mOTUs-db name of the genome</code> <code>    SOURCE_SAMPLE_LINK → Link to the original location of this genome</code> Example: <code>    #GENOME                                     SOURCE_SAMPLE_LINK</code> <code>    --------------------------------------------------------------------------------------------------------</code> <code>    JGIG23-1_GA0055041_GENO_10000001            https://gold.jgi.doe.gov/analysis_project?id=Ga0055041</code> <code>    RSGB23-1_GCA-006717865-V1_GENO_10000001     https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_006717865.1</code> Supplementary Table 3: A list of all metagenomic studies processed for the mOTUs-db, their number of samples, the number of reconstructed MAGs and the associated publication. Columns: <code>    STUDY       --> Unique mOTUs-db study identifier</code> <code>    BIOPROJECT  --> Public identifier (NCBI/JGI) of metagenomic sequencing project</code> <code>    SAMPLES     --> Number of metagenomic samples</code> <code>    MAGs        --> Number of reconstructed MAGs</code> <code>    PUBLICATION --> Link to publication</code> Example: <code>    STUDY        BIOPROJECT    SAMPLES    MAGs     PUBLICATION</code> <code>    -------------------------------------------------------------------------------------------------</code> <code>    ACIN21-1     PRJEB44456    58         1,110    https://www.nature.com/articles/s42003-021-02112-2</code> Supplementary Table 4: Mapping between mOTUs-db sample identifier, the associated biosample and the environment. Columns: <code>    SAMPLE             --> Unique mOTUS-db sample identifier</code> <code>    BIOSAMPLE          --> Public identifier (NCBI/JGI) of metagenomic sample</code> <code>    STUDY              --> Unique mOTUs-db study identifier</code> <code>    ENVIRONMENT        --> Environment of metagenomic sample</code> <code>    SOURCE_SAMPLE_LINK --> Link to the original location of this sample</code> Example: <code>    #SAMPLE                      BIOSAMPLE     STUDY    ENVIRONMENT  SOURCE_SAMPLE_LINK</code> <code>    ---------------------------------------------------------------------------------------------------------------------</code> <code>    ACIN21-1_SAMN05421555_METAG  SAMN05421555  ACIN21-1 marine       https://www.ncbi.nlm.nih.gov/biosample/SAMN05421555/</code> Supplementary Table 5: A list of environments covered in the mOTUs-db mapped to the respective NCBI taxonomy (if possible) Columns: <code>    TERM             --> Unique environment name</code> <code>    NCBI TAXONOMY ID --> Link to the NCBI taxonomy</code> Example: <code>    TERM                          NCBI TAXONOMY ID</code> <code>    ----------------------------------------------</code> <code>    activated sludge metagenome   NCBI:txid942017</code> <code>    air metagenome                NCBI:txid655179</code>

opencc-by-4.0Nov 2015View details →

Fig. 2 in Eco-taxonomic profile of an iconic vermicomposter - the 'African Nightcrawler' earthworm, Eudrilus eugeniae (Kinberg, 1867)

Fig. 2. Eudrilus eugeniae: (a) ventral view of Qld specimen, (b) vasa deferentia unite to form the muscular euprostates ducting to the centre of the copulatory chamber (characteristic Y-shaped gland on rhs ducts to lhs), (c) 'spermathecal' aperture and combined oviduct (unravelled) to ovisac opposite saccular gland at junction of duct and 'ampulla' (ovary not shown), (d) prostomium, (e) calciferous glands, hearts and dorsal vessel, (f) dorso-lateral view of caudal segments narrowing to pygomere, (g) cocoon. BoXed are: Perrier's (1872: figs 27, 28, 30) figures of male organs – with penis both retracted and everted – plus an enlargement of a seta (his fig. 29 differs somewhat in its internal organ details); Michaelsen's (1892: fig. 10) figure of female organs also showing ovary "ov" (or ovisac?) on 12/13; plus Beddard's (1895: fig. 30) figure of male organs with glandular appendices to bursa copulatriX sometimes fused to form a "single horseshoe-shaped" appendiX neXt to what Eisen (1900: fig. 44) called the silk-producing "Y-shaped gland" (indicated as "Y-sg").

opencc-by-4.0Nov 2015View details →

Fig. 3 in Eco-taxonomic profile of an iconic vermicomposter - the 'African Nightcrawler' earthworm, Eudrilus eugeniae (Kinberg, 1867)

Fig. 3. Distribution map from Michaelsen (1903: chart 1) (hash marks family distribution). Note that New Zealand was in error but other records outside its West African homeland are due mainly to human transportation and the worm's acclimatisation; early Caribbean and Latin American introductions possibly relate to the 16th – 19th century Atlantic slave trade.

opengpl-3.0-or-laterOct 2023View details →

mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene

mTAGs is a tool for the taxonomic profiling of metagenomes. It detects sequencing reads belonging to the small subunit of the ribosomal RNA (SSU-rRNA) gene and annotates them through the alignment to full-length degenerate consensus SSU-rRNA reference sequences. The tool is capable of processing single-end and pair-end metagenomic reads, takes advantage of the information contained in any region of the SSU-rRNA gene and provides relative abundance profiles at multiple taxonomic ranks (Domain, Phylum, Class, Order, Family, Genus and OTUs defined at a 97% sequence identity cutoff).

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In silico mock communities for evaluation of taxonomic profilers across prokaryotes and viruses

In silico mock communities generated with CAMISIM for benchmarking the performance of taxonomic profilers across prokaryotic (50 communities), eukaryotic (30 communities), and viral communities (10 communities) of the human microbiome. Metagenomes were generated using CAMISIM (Fritz et al., 2019), which simulates 2.1 Gb of Illumina 2 ×150 bp paired end reads with the default HiSeq 2500 error profile and a mean insert size of 200 bp. To assess profiling performance for a range of sequencing depths, the 50 in silico metagenomes were also rarefied with seqtk (-s100) to sequencing depths of 20, 5, 2, 1, 0.5, 0.25 and 0.1 million read pairs. Counts are provided for rarefied metagenomes. Prokaryotic communities For prokaryotic benchmarking, 10 body site-representative prokaryotic metagenomes were simulated for each of the following five body sites: adult gut, infant gut, oral, skin, and vagina. Genome accession ids for prokaryotic species found in each human body site were identified from published literature (Bäckhed et al., 2015; Proctor et al., 2019; Saheb Kashaf et al., 2021).  Adult Gut: pro_gut_adult.zip Infant Gut: pro_gut_infant.zip Oral: pro_oral.zip Skin: pro_skin_1.zip, pro_skin_2.zip, pro_skin_3.zip Vaginal: pro_vaginal.zip Downsized counts:  Eukaryotic communities 30 eukaryotic in silico metagenomes comprising up to 200 randomly sampled genomes from a set of 113 eukaryotic species (See Supplementary Table 2 from the paper) corresponding to the eukaryotic species within both CHAMP and MetaPhlAn 4 (Blanco-Míguez et al., 2023) databases. Eukaryotic data is deposited here: <a href="https://doi.org/10.5281/zenodo.12090449" target="_blank" rel="noopener">doi: 10.5281/zenodo.12090449</a> Viral communities 10 viral communities were simulated with 95% of the reads from bacteria and 5% of the reads originating from phages. Each community consisted of 200 randomly selected bacterial genomes from GTDB with species-level annotation and 200 viral genomes from the Gut Phage Database (GPD, Camarillo-Guerrero et al., 2021).  Counts: phage_communities_counts.zip FastQ, forward reads: camisimu_[1-10].fq.1.gz FastQ, reverse reads: camisimu_[1-10].fq.2.gz References Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., et al. (2015). Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe 17, 690–703. doi: 10.1016/J.CHOM.2015.04.004 Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology 2023 41:11 41, 1633–1644. doi: 10.1038/s41587-023-01688-w Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D., and Lawley, T. D. (2021). Massive expansion of human gut bacteriophage diversity. Cell 184, 1098. doi: 10.1016/J.CELL.2021.01.029 Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., et al. (2019). CAMISIM: Simulating metagenomes and microbial communities. Microbiome 7, 1–12. doi: 10.1186/S40168-019-0633-6/FIGURES/5 Proctor, L. (2019). Priorities for the next 10 years of human microbiome research. Nature 2021 569:7758 569, 623–625. doi: 10.1038/d41586-019-01654-0 Saheb Kashaf, S., Proctor, D. M., Deming, C., Saary, P., Hölzer, M., Mullikin, J., et al. (2021). Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Nature Microbiology 2021 7:1 7, 169–179. doi: 10.1038/s41564-021-01011-w

opencc-by-4.0Jun 2024View details →

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Fig. 1. A Eudrilus eugeniae specimen from a in Eco-taxonomic profile of an iconic vermicomposter - the 'African Nightcrawler' earthworm, Eudrilus eugeniae (Kinberg, 1867)

Fig. 1. A Eudrilus eugeniae specimen from a vermicompost site.

opencc-by-4.0Nov 2015View details →

mOTUs 1.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: mOTUs SoftwareVersion: 1.1 DataURL: https://data.cami-challenge.org/participate SoftwareURL: http://www.bork.embl.de/software/mOTUs1/ DockerImage: stefanjanssen/docker_profiling_tools:motu IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: mOTU.v1.padded ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:motu

FOCUS 0.31 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: FOCUS SoftwareVersion: 0.31 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/metageni/FOCUS DockerImage: stefanjanssen/docker_profiling_tools:focus IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: k8_bacterial_and_draft ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:focus

MetaPhlAn 2.9.21 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPhlAn SoftwareVersion: 2.9.21 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://bitbucket.org/biobakery/metaphlan2 DockerImage: cami/metaphlan:2.9.21 IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: mpa_v29_CHOCOPhlAn_201901 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ --volume="/path/to/reference_database:/exchange/db:rw" \ cami/metaphlan:2.9.21

MetaPhlAn 2.2.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPhlAn SoftwareVersion: 2.2.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://bitbucket.org/biobakery/metaphlan2 DockerImage: stefanjanssen/docker_profiling_tools:metaphlan2 IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: mpa_v20_m200 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:metaphlan2

CAMIARKQuikr 1.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: CAMIARKQuikr SoftwareVersion: 1.0.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://doi.org/10.5281/zenodo.1730572 DockerImage: stefanjanssen/docker_profiling_tools:quickr IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: https://doi.org/10.5281/zenodo.1730572 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:quickr

MetaPhyler 1.25 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: MetaPhyler SoftwareVersion: 1.25 DataURL: https://data.cami-challenge.org/participate SoftwareURL: http://metaphyler.cbcb.umd.edu/ DockerImage: stefanjanssen/docker_profiling_tools:metaphyler IsBiobox: True BioboxYAMLFile: https://zenodo.org/record/3629567/files/biobox.yaml?download=1 ReferenceDatabase: 2012 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: docker run \ --volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \ --volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \ --volume="/path/to/output:/bbx/mnt/output:rw" \ --volume="/path/to/output/metadata:/bbx/metadata:rw" \ --volume="/path/to/output/cache:/cache:rw" \ stefanjanssen/docker_profiling_tools:metaphyler

mOTUs 2.5.1 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63

Software: mOTUs SoftwareVersion: 2.5.1 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://motu-tool.org/ DockerImage: cami/motus:2.5.1 IsBiobox: False ReferenceDatabase: mOTUs database version 2.5.0 ShortReadsUsed: True LongReadsUsed: False CommandsUsed: for i in {0..63}; do motus profile -f sample_$((i))/reads/anonymous_reads_r1.fq -r sample_$((i))/reads/anonymous_reads_r2.fq -n $((i)) -C precision > sample$((i)).profile ; done cat sample*.profile > cami2_mouse_gut_motus2.5.1.profile

opencc-by-4.0Jun 2021View details →

Taxonomic profiles of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness

Taxonomic profiles including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness. See <a href="https://www.microbiome-cosi.org/cami">https://www.microbiome-cosi.org/cami</a> and <a href="https://data.cami-challenge.org/participate">https://data.cami-challenge.org/participate</a>.