Output files

Log output:

1. log_project.txt

This is a basic log file with the information that shows up on your terminal.

2. log_extented_project.txt

This file will only be generated when the "Extended log" option in the config file is set to "1".
It is a elaborate log file that can be send to me for troubleshooting, it won't provide the user additional info.

Assembly output:

1. Contigs_project.txt

This file contains all the assembled contigs.

2a. Circularized_assembly_project.fasta

When NOVOPlasty is able to circularize one contig, without any additional contigs being produced, it will just output this circularized fasta file.

OR

2b1. Merged_contigs_project.txt

When there are multiple contigs, NOVOPlasty will try to combine all contigs in to a complete circular genome, all the different possibilities can be found in this file.

2b2. Option_nr_project.txt

All possible contig combinations will have a seperate fasta file.

3. contigs_tmp_project.txt

If non of the above files are outputted or are empty, you can retrieve some contigs from this file.

Variance output:

1. Variance_project.vcf

When the variance detection option is selected, an additional vcf file will be outputted.

Heteroplasmy output:

1. Heteroplasmy_project.vcf

This vcf file contains all the detected heteroplasmy positions.

2. Heteroplasmy_assemblies_project.fasta

NOVOPlasty will assemble around each position of the above vcf output.
The resulting assemblies will be outputted in this fasta file.

3. Linkage_table_heteroplasmy_project.txt

This file contains all the polymorphisms that are fully/partially/not linked with each detected heteroplasmic position.

4. Possible_NUMTs_project.vcf / Possible_NUMTs_assemblies_project.fasta / Linkage_table_NUMTs_project.txt

These are the same files as the above three, but then for all the polymorphisms that were identified as NUMT origin.

5. Circos_mutations_project.txt / Circos_links_project.txt

These files can be used to draw figures with Circos. See "Circos Figures" section.