GetOrganelle v1.7.3.2

improve support for standard gfa format: E/L with optional fields

GetOrganelle v1.7.3.1

1. bug fixed: a bug of sorting consensus vertex names using smart_trans_for_sort
2. option --max-reads inf configured

GetOrganelle v1.7.3

1. Add fungus_nr mode.
2. Relocate default GetOrganelle databases using shell environment value GETORG_PATH or "~/.GetOrganelle" by default
3. --reverse-lsc malfunction issue solved
4. slim_graph.py: add --evalue

GetOrganelle v1.7.2

1. slim_graph.py: fix a bug in parsing options
2. automatically adding --phred-offset to avoid hammer failures
3. MergingHistory and ConsensusHistory added, in replace of using the names to detect merging history
4. Compatible with flye gfa format
5. Scaffolding function bug fixed & improved
6. get_organelle_config.py: example typo fixed

GetOrganelle v1.7.1-meta

--meta added for testing

Quickly try this version using:

conda install -c biojj -c bioconda GetOrganelle=1.7.1meta

GetOrganelle v1.7.1

1. Assembly.get_all_circular_paths(): optimized for plastome order - starting from the "single copy contigs at branching points" rather than the previous "largest single copy contig"; the whole potential lsc region are now taking into account for orfs counting for output orientation.
2. get_organelle_from_reads.py: 1) --ignore-k work for small k disentanglement; 2) fix a bug when input reads are very few; 3) better log info
3. get_organelle_from_assembly.py: 1) do not convert gfa to fastg during sub-steps; 2) better log info
4. Assembly.reduce_to_subgraph: limit_offset_current_vertex -> bait_offsets, the former was a risky setting of slim_graph.py since 1.7.0 because of --max-slim-extending-len added, now issue solved.
5. Utilities/slim_fastg.py: fix a bug with anonym mode
6. README.md: updated

GetOrganelle v1.7.0

1. use SPAdes generated scaffolds.paths to create gap containing scaffolds (assembly_parser.py)
2. get_organelle_config.py added with GetOrganelleLib/*Database removed
3. slim_graph.py optimized with --max-slim-extending-len added
4. fix bugs

GetOrganelle v1.6.4

Latest updates:

1. conda installation
2. isolate GetOrganelleDep
3. log plastome structure
4. --max-paths-num added
5. evaluate_assembly_using_mapping.py: --stat-mode, --bowtie2-options, --plot-font added

GetOrganelle v1.6.3a

1.6.3 updates:

1. --max-multiplicity added
2. fix a bug when kmer-len repeats shared by two contigs; fix a bug that cause RuntimeError
3. Assembly.parse_gfa(): compatibility increased
4. Assembly.estimate_copy_and_depth_precisely(): fix a bug on a rare case that multiplicities res are 4,8,4
5. Assembly: too many results due to palindromic repeats, problem solved

see GetOrganelleLib/versions.py for more details

GetOrganelle v1.6.2e

1.6.2e

1. seq_parser.py: fix a bug for fastq format: @*****#/1
2. get_organelle_from_reads.py: separate_fq_by_pair(), fix a bug when detecting pair info failed;
3. evaluate_assembly_using_mapping.py: fix a bug for --plot-transparent
4. GetOrganelleLib.__init__.py: __version__
5. README.md: updated

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