Description

Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

FASTA file of assembled contigs.

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

Output

name:type
description
pattern

classifications{:bash}

meta{:bash}

:map

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

${prefix}.{txt,txt.gz}{:bash}

:file

TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag —gz is set.

*.{txt,txt.gz}

log{:bash}

meta{:bash}

:map

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

log_*.{txt,txt.gz}{:bash}

:file

Log file containing tiara model parameters. Gzipped if flag —gz is set.

log_*.{txt,txt.gz}

fasta{:bash}

meta{:bash}

:map

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

*.{fasta,fasta.gz}{:bash}

:file

(optional) - fasta files for each domain category specified in command flag -tf, containing classified contigs

*.{fasta,fasta.gz}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

tiara
MIT

Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch.

ibe-uw.github.io/tiara ibe-uw.github.io/tiara/" https://github.com/ibe-uw/tiara 10.1093/bioinformatics/btab672
included in
genomeqcmag
maintainer
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