NOVOPlasty files

1. NOVOPlasty3.2.pl

This is the main script to run NOVOPlasty:

perl NOVOPlasty3.2.pl -c config.txt

2. config.txt

This is the configuration file. All the necessary parameters need to be adjusted before you run NOVOPlasty. For more detail check the section of the configuration file.

3. Seed_RUBP_cp.fasta

This is an example of a seed file for chloroplast assembly, can be used for most of the species.

4. filter_reads.pl

This script can filter organelle reads from a large WGS dataset. Although you need a very close reference sequence. This can be useful for heroplasmy detection.

perl filter_reads.pl -1 forward_reads.fastq -2 reverse_reads.fastq -ref reference_sequence.fasta -out project_name

5. Circos folder

5.1 Circos_human_anno.txt / Circos_human_anno2.txt

These files can be used to include annotation in the Circos figure.
The positions of the genes are based on the human reference mitochondrial genome and will not work for any other sequence.
If you have the annotation of a different mitochondrial genome, it is possible to adjust these files accordingly.

5.2 bands.conf / ideogram.position.conf / ticks.conf

These files are from the Circos program and have to be placed in the /bin folder

6. Test datasets

6.1 Chloroplast assembly

These folder contains all the files needed to try out a chloroplast assembly of a Oryza sativa dataset

6.2 Mitochondrial assembly

These folder contains all the files needed to try out a mitochondrial assembly of a human dataset