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

CAT 4.6 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: CAT SoftwareVersion: 4.6 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/dutilh/CAT ReferenceDatabase: prebuilt 2018-12-12 Taxonomy: NCBI 2018-12-12 ShortReadsUsed: False LongReadsUsed: False CommandUsed: CAT contigs -c anonymous_gsa_pooled.fasta -d CAT_prepare_20181212/2018-12-12_CAT_database/ -t CAT_prepare_20181212/2018-12-12_taxonomy/ --tmpdir tmp --nproc 16

PhyloPythiaS+ 1.4 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: PhyloPythiaS+ SoftwareVersion: 1.4 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/algbioi/ppsp DockerImage: cami/ppsp:1.4 IsBiobox: False ReferenceDatabase: RefSeq 93, SILVA 132 Taxonomy: NCBI 2018-02-26 ShortReadsUsed: False LongReadsUsed: False CommandUsed: run_ppsp.py --pipelineDir ppsp_pipepline --inputFastaFile anonymous_gsa_pooled.fasta --databaseFile ncbi_taxonomy --refSeq refseq93 --s16Database SILVA_132 --mgDatabase reference_NCBI201502/mg5

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

MetaBAT 2.12.1 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly Software: MetaBAT SoftwareVersion: 2.12.1 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://bitbucket.org/berkeleylab/metabat ShortReadsUsed: True LongReadsUsed: False CommandUsed: bowtie2-build anonymous_gsa_pooled.fasta anonymous_gsa_pooled.fasta for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done runMetaBat.sh -l anonymous_gsa_pooled.fasta anonymous_reads_sample_*.sorted.bam

Kraken 2.0.8 beta taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: Kraken SoftwareVersion: 2.0.8 beta DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://ccb.jhu.edu/software/kraken2/ ReferenceDatabase: built 2019-05-22 Taxonomy: NCBI 2019-05-22 ShortReadsUsed: False LongReadsUsed: False CommandUsed: kraken2-build --standard --db kraken2db_std --use-ftp kraken2 --db kraken2db_std --threads 16 --output 19122017_mousegut_scaffolds.kraken --report 19122017_mousegut_scaffolds.kreport anonymous_gsa_pooled.fasta cat 19122017_mousegut_scaffolds | awk '{print $2 "\t" $3}' > 19122017_mousegut_scaffolds.cami

zenodo36/100

Biobox YAML file for the CAMI 2 Mouse Gut Toy data set, samples 0-63

Biobox YAML file for the CAMI 2 Mouse Gut Toy data set, samples 0-63

opencc-by-4.0Feb 2020View details →

zenodo36/100

Average genome coverage of the CAMI 2 Mouse Gut Toy data set

Genome coverage (short reads) averaged over the 64 samples of the CAMI 2 Mouse Gut Toy data set

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

DAS Tool 1.1.2 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly. Refinement of the binning output of MaxBin 2.2.7, MetaBAT 2.12.1, CONCOCT 1.0.0, and DAS Tool 1.1.2. Software: DAS Tool SoftwareVersion: 1.1.2 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/cmks/DAS_Tool DockerImage: cami/das_tool:1.1.2 IsBiobox: No ShortReadsUsed: True LongReadsUsed: False CommandUsed: DAS_Tool -i binning_concoct1.0.0,binning_maxbin2.2.7,binning_metabat2.12.1 -c anonymous_gsa_pooled.fasta -o output --search_engine diamond

CONCOCT 1.0.0 genome binning of the CAMI 2 Mouse Gut Toy data set, samples 0-63, gold standard pooled assembly

Genome binning of the gold standard pooled assembly Software: CONCOCT SoftwareVersion: 1.0.0 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/BinPro/CONCOCT DockerImage: quay.io/biocontainers/concoct:1.0.0--py37h88e4a8a_5 IsBiobox: No ShortReadsUsed: True LongReadsUsed: False CommandUsed: for i in {0..63}; do bowtie2 -q --threads 30 --fr -x anonymous_gsa_pooled.fasta --interleaved sample_${i}/anonymous_reads.fq -S anonymous_reads_sample_${i}.sam ; done for i in {0..63}; do samtools view -b sample_${i}.sam -o anonymous_reads_sample_${i}.bam & done for i in {0..63}; do samtools sort anonymous_reads_sample_${i}.bam -o anonymous_reads_sample_${i}.sorted.bam ; done for i in {0..63}; do samtools index anonymous_reads_sample_${i}.sorted.bam ; done cut_up_fasta.py anonymous_gsa_pooled.fasta -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa concoct_coverage_table.py contigs_10K.bed /host/benchmarking/fmeyer/output/bowtie2/mouse_gut/sorted_bam/anonymous_reads_sample_*.sorted.bam > coverage_table.tsv concoct --composition_file contigs_10K.fa --coverage_file coverage_table.tsv -b merge_cutup_clustering.py clustering_gt1000.csv > clustering_merged.csv

MEGAN 6.15.2 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: MEGAN SoftwareVersion: 6.15.2 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/husonlab/megan-ce ReferenceDatabase: NCBI nr 2019-04-17 Taxonomy: NCBI 2019-04-17 ShortReadsUsed: False LongReadsUsed: False CommandUsed: diamond makedb --in nr.faa.gz --db nr_diamond0.9.24 --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp diamond blastx -d nr_diamond0.9.24 -q anonymous_gsa_pooled.fasta -a result -t tmp --index-chunks 1 megan/tools/daa2rma -i result.daa -o 19122017_mousegut_scaffolds.rma --acc2taxa megan/prot_acc2tax-Nov2018X1.abin #final bins extracted with MEGAN's graphical interface tool

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

DIAMOND 0.9.24 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly

Taxonomic binning of the gold standard pooled assembly Software: DIAMOND SoftwareVersion: 0.9.24 DataURL: https://data.cami-challenge.org/participate SoftwareURL: https://github.com/bbuchfink/diamond ReferenceDatabase: NCBI nr 2019-04-17 Taxonomy: NCBI 2019-04-17 ShortReadsUsed: False LongReadsUsed: False CommandUsed: diamond makedb --in nr.faa.gz --db nr --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp diamond blastx --query anonymous_gsa_pooled.fasta --db nr --outfmt 102 --out 19122017_mousegut_scaffolds.out --block-size 40 --index-chunks 1 --tmpdir tmp

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