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Releases: Kinggerm/GetOrganelle

GetOrganelle v1.6.2d

02 Aug 17:42
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1.6.2d

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

1.6.2c

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

1.6.2b

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

1.6.2a

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

GetOrganelle v1.6.2

29 Jun 06:11
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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.

GetOrganelle v1.6.1

13 Jun 08:53
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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.

GetOrganelle v1.6.0

11 Jun 02:35
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  1. This version of GetOrganelle is able to assemble multiple organelle genomes (including plant plastomes, plant, animal, fungal mitogenomes) in one run.
  2. Dependencies (SPAdes, NCBI-blast+, Bowtie2) now are attached, which makes GetOrganelle easier to install.
  3. The extending length from the seed could be roughly controlled with option "max-extending-len".
  4. get_organelle_from_assembly.py is created for easier treatment of assembly graph files.

GetOrganelle v1.5.2

29 Mar 09:25
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version tested in GetOrganelle paper

GetOrganelle v1.5.1c

23 Mar 23:55
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GetOrganelle v1.5.1b

28 Feb 02:44
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GetOrganelle v1.4.4b

04 Dec 06:05
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fix a bug of single-contig graph on v1.4.4a

GetOrganelle v1.4.4a

02 Dec 14:39
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Better disentangling for both circular genomes and contigs.

GetOrganelle v1.4.0j

28 Oct 03:38
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Restore the default settings.