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GetOrganelle v1.6.2

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@Kinggerm Kinggerm released this 29 Jun 06:11
· 272 commits to master since this release

Broader utility:
a) Organelle types: plant_pt, plant_mt, plant_nr, fungus_mt, animal_mt, anonym
b) Be able to assemble multiple organelle genomes in one run.
c) The extending length from the seed could be roughly controlled (--max-extending-len).
d) get_organelle_from_assembly.py is created for easier treatment of assembly graph files.
Easier to install:
a) pip install GetOrganelle
b) Dependencies (SPAdes, NCBI-blast+, Bowtie2) now are attached
Accurate/Convenient:
a) -F embplant_pt does not remove embplant_mt-hitting contigs, which makes more accurate clustering.
b) For embplant_pt, the output plastome would have conventional LSC orientation if there is no structural variation.

Several bugs fixed:
a) high version of blastn not executable in some linux system.
b) '-h' error in get_organelle_from_assembly.py
c) other minor bugs.