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}
:file
FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin
*.tsv
proteins{:bash}
:file
Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
*.{fa.gz,fas.gz,fasta.gz}
db_directory{:bash}
:file
(optional) Directory of single copy gene database.
Output
name:type
description
pattern
log{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.log{:bash}
:file
Log file of the run
*.log
summary{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_summary.tsv{:bash}
:file
Summary of output bins including quality and completeness estimates
*summary.txt
contig2bin{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_DASTool_contig2bin.tsv{:bash}
:file
Scaffolds to bin file of output bins
*.contig2bin.txt
eval{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.eval{:bash}
:file
Quality and completeness estimates of input bin sets
*.eval
bins{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_DASTool_bins/*.fa{:bash}
:file
Final refined bins in fasta format
*.fa
pdfs{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.pdf{:bash}
:file
Plots showing the amount of high quality bins and score distribution of bins per method
*.pdf
candidates_faa{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.candidates.faa{:bash}
:file
FAA file
*.candidates.faa
fasta_proteins{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_proteins.faa{:bash}
:file
Output from prodigal if not already supplied
*_proteins.faa
fasta_archaea_scg{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.archaea.scg{:bash}
:file
Results of archaeal single-copy-gene prediction
*.archaea.scg
fasta_bacteria_scg{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.bacteria.scg{:bash}
:file
Results of bacterial single-copy-gene prediction
*.bacteria.scg
b6{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.b6{:bash}
:file
Results in b6 format
*.b6
seqlength{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.seqlength{:bash}
:file
Summary of contig lengths
*.seqlength
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
dastool
BSD
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.
