Description

A python workflow that assembles mitogenomes from Pacbio HiFi reads

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

Path to PacBio HiFi reads or fasta contigs

*.{fa,fa.gz,fasta,fasta.gz}

meta2{:bash}

:map

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

ref_fa{:bash}

:file

Reference mitochondrial genome to align reads or contigs against

*.{fa,fasta}

meta3{:bash}

:map

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

ref_gb{:bash}

:file

Reference mitochondrial genome annotation

*.{gb}

input_mode{:bash}

:string

Specifies type of input - reads or contigs

{reads,contigs}

mito_code{:bash}

:integer

Integer reference number of mitochondrial genetic code - see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details.

Output

name:type
description
pattern

fasta{:bash}

meta{:bash}

:map

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

final_mitogenome.fasta{:bash}

:file

Fasta file containing final chosen mitochondrial sequence

final_mitogenome.fasta

stats{:bash}

meta{:bash}

:map

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

contigs_stats.tsv{:bash}

:file

Statistics of all identified mitochondrial contigs

contigs_stats.tsv

gb{:bash}

meta{:bash}

:map

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

final_mitogenome.gb{:bash}

:file

GB annotation file of final chosen mitochondrial sequence, if Mitofinder mode was used for annotation.

final_mitogenome.gb

gff{:bash}

meta{:bash}

:map

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

final_mitogenome.gff{:bash}

:file

GB annotation file of final chosen mitochondrial sequence, if Mitos mode was used for annotation.

final_mitogenome.gff

all_potential_contigs{:bash}

meta{:bash}

:map

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

all_potential_contigs.fa{:bash}

:file

Fasta file containing sequences of all potential mitogenome contigs

all_potential_contigs.fa

contigs_annotations{:bash}

meta{:bash}

:map

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

contigs_annotations.png{:bash}

:file

Graphical representation of annotated genes and tRNAs

contigs_annotations.png

contigs_circularization{:bash}

meta{:bash}

:map

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

contigs_circularization/{:bash}

:directory

Contains circularization reports

contigs_circularization/

contigs_filtering{:bash}

meta{:bash}

:map

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

contigs_filtering/{:bash}

:directory

Contains files with initial blast matches

contigs_filtering/

coverage_mapping{:bash}

meta{:bash}

:map

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

coverage_mapping/{:bash}

:directory

Contains statistics on coverage mapping

coverage_mapping/

coverage_plot{:bash}

meta{:bash}

:map

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

coverage_plot.png{:bash}

:file

Read coverage plot for mitochondrial contigs

coverage_plot.png

final_mitogenome_annotation{:bash}

meta{:bash}

:map

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

final_mitogenome.annotation.png{:bash}

:file

Graphical representation of annotated genes for the final mitogenome contig

final_mitogenome.annotation.png

final_mitogenome_choice{:bash}

meta{:bash}

:map

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

final_mitogenome_choice/{:bash}

:directory

Files with potential contigs clusterings and alignments

final_mitogenome_choice/

final_mitogenome_coverage{:bash}

meta{:bash}

:map

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

final_mitogenome.coverage.png{:bash}

:file

Graphical representation of reads coverage plot for the final mitogenome contig

final_mitogenome.coverage.png

potential_contigs{:bash}

meta{:bash}

:map

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

potential_contigs/{:bash}

:directory

Files with sequences and annotations of the potential contigs

potential_contigs/

reads_mapping_and_assembly{:bash}

meta{:bash}

:map

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

reads_mapping_and_assembly/{:bash}

:directory

Read mapping files for run from the raw reads

reads_mapping_and_assembly/

shared_genes{:bash}

meta{:bash}

:map

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

shared_genes.tsv{:bash}

:directory

Report on genes shared with the reference genome

shared_genes.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

mitohifi.py
MIT

A python workflow that assembles mitogenomes from Pacbio HiFi reads

github.com/marcelauliano/MitoHiFi 10.1101/2022.12.23.521667
maintainer
Github user ksenia-krasheninnikova
get in touch
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