Description

A python workflow that assembles mitogenomes from Pacbio HiFi reads

Input

Name (Type)
Description
Pattern

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}

code (integer)

Mitochndrial code for annotation

[0-9]*

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

fasta (file)

Mitochondrial sequence

*.{fasta,fa}

gb (file)

Genome annotation in case mitofinder was used

*.gb

gff (file)

Genome annotation in case mitos was used

*.gff

all_potential_contigs (file)

Contains sequences of all potential contigs

*all_potential_contigs.fa

contigs_annotations (file)

Graphical representation of annotated genes and tRNAs

*contigs_annotations.png

contigs_circularization (directory)

Contains circularization reports

*contigs_circularization

contigs_filtering (directory)

Contains files with initial blast matches

*contigs_filtering

coverage_mapping (directory)

Contains statistics on coverage mapping

*coverage_mapping

coverage_plot (file)

Read coverage plot for mitochondrial contigs

*coverage_plot.png

final_mitogenome_annotation (file)

Graphical representation of annotated genes for the final mito contig

*final_mitogenome.annotation.png

final_mitogenome_choice (directory)

Files with potential contigs clusterings and alignments

*final_mitogenome_choice

final_mitogenome_coverage (file)

Graphical representation of reads coverage plot for the final mito contig

*final_mitogenome.coverage.png

potential_contigs (directory)

Files with sequences and annotations of the potential contigs

*potential_contigs

reads_mapping_and_assembly (directory)

Read mapping files for run from the raw reads

*reads_mapping_and_assembly

shared_genes (directory)

Report on genes shared with the reference genome

*shared_genes.tsv

versions (file)

Software versions used in the run

versions.yml
maintainer
Github user ksenia-krasheninnikova
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

mitohifi.py
MIT

A python workflow that assembles mitogenomes from Pacbio HiFi reads

github.com/marcelauliano/MitoHiFi 10.1101/2022.12.23.521667