mitomine is a bioinformatics pipeline for mitochondrial genome assembly from next-generation sequencing (NGS) data.
The pipeline performs the following main steps:
- Mitochondrial Genome DENOVO Assembly (NovoPlasty)
- Mitochondrial Genome Ref Assembly (MitoZ)
- Annotation
Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with
-profile testbefore running the workflow on actual data.
To run a quick test and verify that everything is set up correctly, execute:
nextflow run mitomine/ -profile <singularity,docker,...>,test --outdir testFirst, prepare a samplesheet with your input data that looks as follows:
samplesheet.csv:
sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Now, you can run the pipeline using:
nextflow run nf-core/mitomine \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>Warning: Please provide pipeline parameters via the CLI or Nextflow
-params-fileoption. Custom config files including those provided by the-cNextflow option can be used to provide any configuration except for parameters; see docs.
For more details and further functionality, please refer to the usage documentation and the parameter documentation.