An nf-core module for the OATK
meta
Groovy Map containing sample information e.g. [ id:‘Cladonia_norvegica’ ]
reads
HiFi reads in FASTA format
*.{fasta,fasta.gz,fa,fa.gz}
mito_hmm
mitochondria gene annotation HMM profile database
*.{fa,fam}
mito_hmm_h3f
mitochondria gene annotation HMM profile binary auxfile
*.{h3f}
mito_hmm_h3i
*.{h3i}
mito_hmm_h3m
*.{h3m}
mito_hmm_h3p
*.{h3p}
pltd_hmm
plastid gene annotation HMM profile database
pltd_hmm_h3f
plastid gene annotation HMM profile binary auxfile
pltd_hmm_h3i
pltd_hmm_h3m
pltd_hmm_h3p
Groovy Map containing sample information e.g. [ id:‘test’, single_end
versions
File containing software versions
versions.yml
mito_fasta
the structure-solved MT contigs
*mito.ctg.fasta
pltd_fasta
the structure-solved PT contigs
*pltd.ctg.fasta
mito_bed
the gene annotation for the MT sequences
*mito.ctg.bed
pltd_bed
the gene annotation for the PT sequences
*pltd.ctg.bed
mito_gfa
the subgraph for the MT genome
*mito.gfa
pltd_gfa
the subgraph for the PT genome
*pltd.gfa
annot_mito_txt
the MT gene annotation file over all assembled sequences
*annot_mito.txt
annot_pltd_txt
the PT gene annotation file over all assembled sequences
*annot_pltd.txt
clean_gfa
the GFA file for the clean genome assembly
*utg.clean.gfa
final_gfa
the GFA file for the final genome assembly
*utg.final.gfa
initial_gfa
the GFA file for the initial genome assembly
*utg.gfa
multiplex_gfa
the mutliplexed GFA file
*utg.multiplex.gfa
unzip_gfa
the unzipped GFA file
*utg.unzip.gfa
An organelle genome assembly toolkit
