Description

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

reads (file)

Channel containing single or paired-end reads

*.{fastq.gz,fq.gz}

sliva_db (directory)

Folder containing the SILVA database

ref

univec_db (directory)

Folder containing UniVec database

UniVec

Output

Name (Type)
Description
Pattern

meta (map)

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

]

results (directory)

Folder containing the results of phyloFlash analysis

${prefix}*

versions (file)

File containing software versions

versions.yml
maintainer
Github user abhi18av
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

phyloflash
GPL v3

phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

hrgv.github.io/phyloFlash hrgv.github.io/phyloFlash/usage https://github.com/HRGV/phyloFlash 10.1128/mSystems.00920-20