Description

NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI’s FCS-adaptor, which is for the same purpose

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘6973’ ]

fasta_file:file

FASTA file that will be screened for contaminants

adapters_database_meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

adapters_database_directory:directory

Directory containing the adapters database

Output

name:type
description
pattern

vecscreen_output

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, taxid:‘9606’ ]

${meta.id}.vecscreen.out:file

VecScreen report file. This can be in different formats depending on the value of the optional -f parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0

*.vecscreen.out

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ncbitools
The Open Database License

"NCBI libraries for biology applications (text-based utilities)"

ncbi.nlm.nih.gov/tools/vecscreen ncbi.nlm.nih.gov/tools/vecscreen/interpretation https://www.ncbi.nlm.nih.gov/tools/vecscreen/
maintainer
Github user eeaunin
get in touch
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