A python workflow that assembles mitogenomes from Pacbio HiFi reads
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input:file
Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified in ext.args2
*.{fa,fa.gz,fasta,fasta.gz}
ref_fa:file
Reference sequence
*.{fa,fasta}
ref_gb:file
Reference annotation
*.{gb}
input_mode:string
Specifies type of input - reads or contigs
{r,c}
mito_code:string
Mitochondrial genetic code
fasta
meta:file
Mitochondrial sequence
*.{fasta,fa}
*fasta:file
stats
*contigs_stats.tsv:file
Contigs statistics
*contigs_stats.tsv
gb
Genome annotation in case mitofinder was used
*.gb
*gb:file
gff
Genome annotation in case mitos was used
*.gff
*gff:file
all_potential_contigs
Contains sequences of all potential contigs
*all_potential_contigs.fa
*all_potential_contigs.fa:file
contigs_annotations
Graphical representation of annotated genes and tRNAs
*contigs_annotations.png
*contigs_annotations.png:file
contigs_circularization
meta:directory
Contains circularization reports
*contigs_circularization
*contigs_circularization:directory
contigs_filtering
Contains files with initial blast matches
*contigs_filtering
*contigs_filtering:directory
coverage_mapping
Contains statistics on coverage mapping
*coverage_mapping
*coverage_mapping:directory
coverage_plot
Read coverage plot for mitochondrial contigs
*coverage_plot.png
*coverage_plot.png:file
final_mitogenome_annotation
Graphical representation of annotated genes for the final mito contig
*final_mitogenome.annotation.png
*final_mitogenome.annotation.png:file
final_mitogenome_choice
Files with potential contigs clusterings and alignments
*final_mitogenome_choice
*final_mitogenome_choice:directory
final_mitogenome_coverage
Graphical representation of reads coverage plot for the final mito contig
*final_mitogenome.coverage.png
*final_mitogenome.coverage.png:file
potential_contigs
Files with sequences and annotations of the potential contigs
*potential_contigs
*potential_contigs:directory
reads_mapping_and_assembly
Read mapping files for run from the raw reads
*reads_mapping_and_assembly
*reads_mapping_and_assembly:directory
shared_genes
Report on genes shared with the reference genome
*shared_genes.tsv
*shared_genes.tsv:directory
versions
versions.yml:file
File containing software versions
versions.yml
