MitoFinder v1.4.2

Note:
I highly recommend the use of the singularity image.
MitoFinder is written in Python2.7 and therefore need specific installations (Python3 being the new default python version)

Updates:

1. New singularity container.
2. Circularisation check was deprecated (involuntarily) and is now functioning again.
3. Illustrative images are now generated for each annotated contigs. For manual installation, you will need to install pillow==6.2.2.

MitoFinder v1.4.1

Minor updates:

1. New singularity container.
2. New -c or --config option allowing to specify the path to another MitoFinder.config file. This can be useful when using the singularity container.
3. SPAdes updated from version 3.13 to 3.15

MitoFinder v1.4

1. Improvement in the tRNA annotation step with the possibility of using ARWEN, MiTFi (default) or tRNAscan-SE 2 for this step.
2. New option -t or -tRNA-annotation to choose between the three tools.
3. New options --min-contig-size and --max-contig-size.
4. Addition of warning/error messages.
5. Some bugs fixed.

MitoFinder v1.3

1. Bugs fixed in NUMT annotation.
2. Improvement in the intron annotation step with the possibility of finding introns in ribosomal RNA genes.
3. Mitochondrial contig are now sorted by hit score (with mtDNA_contig_1 having a better score than mtDNA_contig_2 ...). Associated new option: --max-hit. This option allows to specify how many contig at most MitoFinder will annotate.
4. New option --rename-contig (to rename or not the contig(s) matching the reference).
5. New option --adjust-direction(to adjust the direction of the contig(s) matching the reference, if necessary).
6. New option --citation(to know how to cite MitoFinder).
7. Some bugs fixed.

MitoFinder v1.2

1. New section in the "README.md" file for installing MitoFinder on Mac OS
2. Addition of a new script named « create_tbl2asn_files.py » to facilitate the submission of the mitochondrial contigs to GenBank (NCBI). + Example cases in a new « NCBI_submission » directory.
3. Addition of a section in the "README.md" file to help users in the submission process.
4. New option –override to facilitate MitoFinder restart.
5. New options for particular cases (--new-genes; --allow-intron; --intron-size; --cds-merge; --numt)
6. New example files
7. Little improvement of the annotation step and TBL files.
8. New output files : [Seq_ID]_mtDNA_contig*_genes_AA.fasta and [Seq_ID]_mtDNA_contig*_genes_NT.fasta for each contig.
9. Some bugs fixed

MitoFinder v1.1

1. Improvement of the annotation step: MitoFinder searches for the start and stop codon. (new option -n)
2. New output file : [job_name]_mtDNA_contig_final.tbl. tbl format is required to submit mtDNA contig on genbank
3. Some bugs fixed

Initial Release (06/01/2019)

v1.0.2

Initial version