MitoHiFi_v3.2.2

1-) mitohifi.py No longer modify input contig file when fixing headers
2-) findMitoReference.py: Updated mito reference script to accept the ncbi api key

MitoHiFi_v3.2.1

1-) When using flag -a funghi, accept contigs larger than reference used, as done for plants.
2-) No extra code change, just changed how to represent contigs_stats.tsv. Now the second line of the file presents the final_mitogenome stats again, but if its original name(contig id). And if MitoHiFi is ran from Hicanu contigs, contigs_stats.tsv will show if the contigs were Hicanu linear or circular by attaching a "l" or "c" to the contig name. Nothing on the True of False logic was changed.

MitoHiFi_v3.2

MitoHiFi_v3.2: (i) fixed --mitos run bug on Docker container by calling to install specifically mitos v2.1.0 on Dockerfile recipe, (ii) structured MitoHiFi code in folders (src, tests..), (iii) created a base Docker image and a code Docker image to update code Docker and build it quicker without needing to install all the dependencies each time, (iv) implemented a integration test to make sure changes on the code don't alter end results, (v) included a badge "passing" for integration test.

MitoHiFi_v3.01

MitoHiFi current release (v3.01). Run within a singularity container or install each dependency. All that is included on v2.2 plus (i) flag --mitos for annotation to be run with MITOS instead of MitoFinder, (ii) shared_genes.tsv file showing comparisons of genes annotated in relation to genes on reference genome, (iii) plots gene annotations for final mito and all potential contigs, (iv) plots coverage mapping, (v) outputs mapped files to be upload to IGV to the folder coverage_mapping, (vi) cdhit allows clustering of large sequences with MAX_SEQ=10000000.

MitoHiFi_v2.2

MitoHiFi current release. Run within a singularity container or install each dependency. It uses the latest version of Hifiasm 0.16.1-r375 and the output contigs_stats.tsv gives you more detailed statistics. It's possible to use this release to circularise, rotate and annotate plant mitochondrion or chloroplast using the flat -a plant (and the flag -t chloroplast for the script findMitoreference.py).

MitoHiFi_v2.1

Dockerfile to create a singularity image for MitoHiFi version 2.1. ATTENTION: This is NOT the most updated version of MitoHiFi. Please go to the master branch and download the latest one there.

MitoHiFi_v1

MitoHifi v1 is based in python and bash. Strongly recommend users to go for v2 as it is much more stable and has many more functionalities.

MitoHiFi_v2.0

MitoHiFi current release. Run within a singularity container or install each dependency.