Description

Assembles organelle genomes from genomic data

Input

Name (Type)
Description
Pattern

meta (map)

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

fastq (file)

Input fastq files

*.{fastq.gz}

organelle_type (string)

Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA)

db (directory)

GetOrganelle database

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

fasta (file)

Complete or partial organelle sequences

*.fasta.gz

etc (file)

Other output files

maintainer
Github user erinyoung
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

getorganelle
GPL v3

Get organelle genomes from genome skimming data

github.com/Kinggerm/GetOrganelle 10.1186/s13059-020-02154-5