Releases · Kinggerm/GetOrganelle

02 Aug 17:42

Kinggerm

v1.6.2d

01bad30

GetOrganelle v1.6.2d

1.6.2d

get_organelle_from_reads.py: fix a bug with "-F anonym"

1.6.2c

GetOrganelleLib/assembly_parser.py: SSC direction set according to orf
disentangle: --reverse-lsc option added; fix a bug for disentangling contigs with no overlaps
Utilities/plastome_arch_info.py: GC content added
get_organelle_from_reads.py: fix a bug for --flush-step inf

1.6.2b

fix a minor bug when raising ProcessingGraphFailed with # tags
setup.py install modified
open() modified

1.6.2a

the bug with option "--genes" fixed
the bug with "Mixing iteration and read methods" introduced by 1.6.2 fixed

Assets 5

29 Jun 06:11

Kinggerm

v1.6.2

60379bc

GetOrganelle v1.6.2

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.

Assets 5

13 Jun 08:53

Kinggerm

v1.6.1

bd9c9b0

GetOrganelle v1.6.1

This version of GetOrganelle is able to assemble multiple organelle genomes (including plant plastomes, plant, animal, fungal mitogenomes) in one run.
New seed sequences were generated with repeats masked.
Dependencies (SPAdes, NCBI-blast+, Bowtie2) now are attached, which makes GetOrganelle easier to install.
The extending length from the seed could be roughly controlled with option "max-extending-len".
get_organelle_from_assembly.py is created for easier treatment of assembly graph files.

Assets 5

11 Jun 02:35

Kinggerm

v1.6.0

757639b

GetOrganelle v1.6.0

This version of GetOrganelle is able to assemble multiple organelle genomes (including plant plastomes, plant, animal, fungal mitogenomes) in one run.
Dependencies (SPAdes, NCBI-blast+, Bowtie2) now are attached, which makes GetOrganelle easier to install.
The extending length from the seed could be roughly controlled with option "max-extending-len".
get_organelle_from_assembly.py is created for easier treatment of assembly graph files.

Assets 5