Description

A python workflow that assembles mitogenomes from Pacbio HiFi reads

Input

name:type
description
pattern

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

Output

name:type
description
pattern

fasta

meta:file

Mitochondrial sequence

*.{fasta,fa}

*fasta:file

Mitochondrial sequence

*.{fasta,fa}

stats

meta:map

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

]

*contigs_stats.tsv:file

Contigs statistics

*contigs_stats.tsv

gb

meta:file

Genome annotation in case mitofinder was used

*.gb

*gb:file

Genome annotation in case mitofinder was used

*.gb

gff

meta:file

Genome annotation in case mitos was used

*.gff

*gff:file

Genome annotation in case mitos was used

*.gff

all_potential_contigs

meta:file

Contains sequences of all potential contigs

*all_potential_contigs.fa

*all_potential_contigs.fa:file

Contains sequences of all potential contigs

*all_potential_contigs.fa

contigs_annotations

meta:file

Graphical representation of annotated genes and tRNAs

*contigs_annotations.png

*contigs_annotations.png:file

Graphical representation of annotated genes and tRNAs

*contigs_annotations.png

contigs_circularization

meta:directory

Contains circularization reports

*contigs_circularization

*contigs_circularization:directory

Contains circularization reports

*contigs_circularization

contigs_filtering

meta:directory

Contains files with initial blast matches

*contigs_filtering

*contigs_filtering:directory

Contains files with initial blast matches

*contigs_filtering

coverage_mapping

meta:directory

Contains statistics on coverage mapping

*coverage_mapping

*coverage_mapping:directory

Contains statistics on coverage mapping

*coverage_mapping

coverage_plot

meta:file

Read coverage plot for mitochondrial contigs

*coverage_plot.png

*coverage_plot.png:file

Read coverage plot for mitochondrial contigs

*coverage_plot.png

final_mitogenome_annotation

meta:file

Graphical representation of annotated genes for the final mito contig

*final_mitogenome.annotation.png

*final_mitogenome.annotation.png:file

Graphical representation of annotated genes for the final mito contig

*final_mitogenome.annotation.png

final_mitogenome_choice

meta:directory

Files with potential contigs clusterings and alignments

*final_mitogenome_choice

*final_mitogenome_choice:directory

Files with potential contigs clusterings and alignments

*final_mitogenome_choice

final_mitogenome_coverage

meta:file

Graphical representation of reads coverage plot for the final mito contig

*final_mitogenome.coverage.png

*final_mitogenome.coverage.png:file

Graphical representation of reads coverage plot for the final mito contig

*final_mitogenome.coverage.png

potential_contigs

meta:directory

Files with sequences and annotations of the potential contigs

*potential_contigs

*potential_contigs:directory

Files with sequences and annotations of the potential contigs

*potential_contigs

reads_mapping_and_assembly

meta:directory

Read mapping files for run from the raw reads

*reads_mapping_and_assembly

*reads_mapping_and_assembly:directory

Read mapping files for run from the raw reads

*reads_mapping_and_assembly

shared_genes

meta:directory

Report on genes shared with the reference genome

*shared_genes.tsv

*shared_genes.tsv:directory

Report on genes shared with the reference genome

*shared_genes.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

mitohifi.py
MIT

A python workflow that assembles mitogenomes from Pacbio HiFi reads