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8 results for “taxonomic binning”
CAT 4.6 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>CAT<br> <strong>SoftwareVersion: </strong>4.6<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/dutilh/CAT<br> <strong>ReferenceDatabase:</strong> prebuilt 2018-12-12<br> <strong>Taxonomy:</strong> NCBI 2018-12-12<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> 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</p>
PhyloPythiaS+ 1.4 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>PhyloPythiaS+<br> <strong>SoftwareVersion: </strong>1.4<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/algbioi/ppsp<br> <strong>DockerImage:</strong> cami/ppsp:1.4<br> <strong>IsBiobox:</strong> False<br> <strong>ReferenceDatabase:</strong> RefSeq 93, SILVA 132<br> <strong>Taxonomy:</strong> NCBI 2018-02-26<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> run_ppsp.py --pipelineDir ppsp_pipepline --inputFastaFile anonymous_gsa_pooled.fasta --databaseFile ncbi_taxonomy --refSeq refseq93 --s16Database SILVA_132 --mgDatabase reference_NCBI201502/mg5</p>
Kraken 2.0.8 beta taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>Kraken<br> <strong>SoftwareVersion: </strong>2.0.8 beta<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://ccb.jhu.edu/software/kraken2/<br> <strong>ReferenceDatabase:</strong> built 2019-05-22<br> <strong>Taxonomy:</strong> NCBI 2019-05-22<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> kraken2-build --standard --db kraken2db_std --use-ftp<br> kraken2 --db kraken2db_std --threads 16 --output 19122017_mousegut_scaffolds.kraken --report 19122017_mousegut_scaffolds.kreport anonymous_gsa_pooled.fasta<br> cat 19122017_mousegut_scaffolds | awk '{print $2 "\t" $3}' > 19122017_mousegut_scaffolds.cami</p>
MEGAN 6.15.2 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>MEGAN<br> <strong>SoftwareVersion: </strong>6.15.2<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/husonlab/megan-ce<br> <strong>ReferenceDatabase:</strong> NCBI nr 2019-04-17<br> <strong>Taxonomy:</strong> NCBI 2019-04-17<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> diamond makedb --in nr.faa.gz --db nr_diamond0.9.24 --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp<br> diamond blastx -d nr_diamond0.9.24 -q anonymous_gsa_pooled.fasta -a result -t tmp --index-chunks 1<br> megan/tools/daa2rma -i result.daa -o 19122017_mousegut_scaffolds.rma --acc2taxa megan/prot_acc2tax-Nov2018X1.abin<br> #final bins extracted with MEGAN's graphical interface tool</p>
DIAMOND 0.9.24 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>DIAMOND<br> <strong>SoftwareVersion: </strong>0.9.24<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/bbuchfink/diamond<br> <strong>ReferenceDatabase:</strong> NCBI nr 2019-04-17<br> <strong>Taxonomy:</strong> NCBI 2019-04-17<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> diamond makedb --in nr.faa.gz --db nr --taxonmap prot.accession2taxid.gz --taxonnodes nodes.dmp<br> diamond blastx --query anonymous_gsa_pooled.fasta --db nr --outfmt 102 --out 19122017_mousegut_scaffolds.out --block-size 40 --index-chunks 1 --tmpdir tmp</p>
Taxonomic binnings of the CAMI 2 Challenge datasets: marine, plant-associated, strain madness
<p>Taxonomic binnings including participant submissions for the CAMI 2 Challenge datasets: marine, plant-associated, strain madness.</p> <p>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>.</p>
FIGURE 1. Agapetes reflexiloba Y. H. Tan & Bin Yang. A–B in Taxonomic studies on Agapetes in Myanmar I: Agapetes reflexiloba, a new species from Kachin State, and notes on three rediscovered species including two new records for Myanmar
FIGURE 1. Agapetes reflexiloba Y. H. Tan & Bin Yang. A–B. Flowering branch; C–D. Inflorescence; E–F. Flower; G. Stamen; H. Flower dissection (from top to bottom and from left to right): corolla, stamen, style along with ovary and pedicel, calyx. Photographed by H.B. Ding & B. Yang.
Gold standard genome and taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Gold standard genome and taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate</p>
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