DAS Tool binning step.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
contigs{:bash}
:file
fasta file
*.{fa.gz,fas.gz,fasta.gz}
bins{:bash}
FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin
*.tsv
proteins{:bash}
Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
db_directory{:bash}
(optional) Directory of single copy gene database.
log{:bash}
*.log{:bash}
Log file of the run
*.log
summary{:bash}
*_summary.tsv{:bash}
Summary of output bins including quality and completeness estimates
*summary.txt
contig2bin{:bash}
*_DASTool_contig2bin.tsv{:bash}
Scaffolds to bin file of output bins
*.contig2bin.txt
eval{:bash}
*.eval{:bash}
Quality and completeness estimates of input bin sets
*.eval
*_DASTool_bins/*.fa{:bash}
Final refined bins in fasta format
*.fa
pdfs{:bash}
*.pdf{:bash}
Plots showing the amount of high quality bins and score distribution of bins per method
*.pdf
candidates_faa{:bash}
*.candidates.faa{:bash}
FAA file
*.candidates.faa
fasta_proteins{:bash}
*_proteins.faa{:bash}
Output from prodigal if not already supplied
*_proteins.faa
fasta_archaea_scg{:bash}
*.archaea.scg{:bash}
Results of archaeal single-copy-gene prediction
*.archaea.scg
fasta_bacteria_scg{:bash}
*.bacteria.scg{:bash}
Results of bacterial single-copy-gene prediction
*.bacteria.scg
b6{:bash}
*.b6{:bash}
Results in b6 format
*.b6
seqlength{:bash}
*.seqlength{:bash}
Summary of contig lengths
*.seqlength
versions_dastool{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
dastool{:bash}
The tool name
DAS_Tool --version 2>&1 | grep "DAS Tool" | sed "s/DAS Tool //"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
The name of the process
The name of the tool
DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
