Description

Screens query sequences against large sequence databases

Input

Name (Type)
Description
Pattern

meta (map)

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

]

query (file)

Query sequences

*.fastq.gz

sequence_sketch (file)

Sequence files to match against

*.msh

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

screen (file)

List of sequences from fastx_db similar to query sequences

*.screen
included in
genomeassembler phageannotator
maintainer
Github user mahesh-panchal
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

mash
https://github.com/marbl/Mash/blob/master/LICENSE.txt

Fast sequence distance estimator that uses MinHash

github.com/marbl/Mash mash.readthedocs.io/en/latest/sketches https://github.com/marbl/Mash 10.1186/s13059-016-0997-x