fraggenescan
Description¶
FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.
Keywords: gene, gene finding, microbial
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install fraggenescan
Tools¶
fraggenescan¶
FragGeneScan is an application for finding (fragmented) genes in short reads.
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
fasta |
file | Database of sequences in FASTA format | *.{fasta,fna,fasta.gz,fna.gz} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
versions |
file | File containing software versions | versions.yml |
nucleotide_fasta |
file | nucleotide sequences file | *.{ffn} |
amino_acid_fasta |
file | protein translations file | *.{faa} |
gene_annotations |
file | gene annotations in plain text | *.out |