combinedgenecaller_merge
Description¶
MGnify merging script for combined gene caller. The merged output contains all the gene predictions from Pyrodigal, along with genes predicted by FragGeneScanRS that do not overlap with any Pyrodigal gene. If mask file is provided, it masks (removes) genes that overlap with regions from a masking file.
Keywords: gene finding, prokaryotes, microbial
Installation¶
ebi-metagenomics/combinedgenecaller/merge
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install combinedgenecaller/merge
Tools¶
combinedgenecaller¶
This script merges the gene prediction with Pyrodigal and FragGeneScanRS
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | - |
pyrodigal_gff |
file | gene annotations in GFF format produced by Pyrodigal | *.gff |
pyrodigal_ffn |
file | nucleotide sequences of genes predicted by Pyrodigal | *.{ffn,fna} |
pyrodigal_faa |
file | protein translations of genes predicted by Pyrodigal | *.faa |
fgs_gff |
file | gene annotations in GFF format produced by FragGeneScanRS | *.gff |
fgs_ffn |
file | nucleotide sequences of genes predicted by FragGeneScanRS | *.{ffn,fna} |
fgs_faa |
file | protein translations of genes predicted by FragGeneScanRS | *.faa |
mask |
file | sequence mask file (tblout files generated by Infernal cmscan or cmsearch) | *.* |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
faa |
file | - | |
ffn |
file | - | |
gff |
file | - | |
versions |
file | - |
People¶
Authors¶
Maintainers