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{:bash}

:map

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

reads{:bash}

:file

Channel containing single or paired-end reads

*.{fastq.gz,fq.gz}

silva_db{:bash}

:directory

Folder containing SILVA database

univec_db{:bash}

:directory

Folder containing UniVec database

UniVec

Output

name:type
description
pattern

results{:bash}

meta{:bash}

:map

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

${meta.id}*/*{:bash}

:directory

Folder containing the results of phyloFlash analysis

${prefix}*

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainer
Github user abhi18av
get in touch
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