Description

DAS Tool binning step.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

contigs:file

fasta file

*.{fa.gz,fas.gz,fasta.gz}

bins:file

FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin

*.tsv

proteins:file

Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)

*.{fa.gz,fas.gz,fasta.gz}

db_directory:file

(optional) Directory of single copy gene database.

Output

name:type
description
pattern

log

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.log:file

Log file of the run

*.log

summary

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_summary.tsv:file

Summary of output bins including quality and completeness estimates

*summary.txt

contig2bin

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_DASTool_contig2bin.tsv:file

Scaffolds to bin file of output bins

*.contig2bin.txt

eval

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.eval:file

Quality and completeness estimates of input bin sets

*.eval

bins

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_DASTool_bins/*.fa:file

Final refined bins in fasta format

*.fa

pdfs

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.pdf:file

Plots showing the amount of high quality bins and score distribution of bins per method

*.pdf

fasta_proteins

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_proteins.faa:file

Output from prodigal if not already supplied

*_proteins.faa

candidates_faa

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.candidates.faa:file

FAA file

*.candidates.faa

fasta_archaea_scg

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.archaea.scg:file

Results of archaeal single-copy-gene prediction

*.archaea.scg

fasta_bacteria_scg

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.bacteria.scg:file

Results of bacterial single-copy-gene prediction

*.bacteria.scg

b6

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.b6:file

Results in b6 format

*.b6

seqlength

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*.seqlength:file

Summary of contig lengths

*.seqlength

versions

versions.yml: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.