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Releases: gtonkinhill/panaroo

v1.5.1

07 Oct 07:55
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  • Added the option to specify 'none' as the aligner, allowing alignment to be run separately as requested in #306.
  • Removed the dependency on the Bio.Applications module, which is going to be deprecated, addressing #301.
  • Exposed the CD-HIT length requirement in the gene family clustering steps to address #299.
  • Bug fixes to address #303.
  • Updated GitHub Actions versions.

v1.5.0

03 Apr 08:07
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  • Adds an option to turn off gene re-finding completely. Users can now choose between three re-finding levels including the original, strict and off.
  • Fixes bug #275, introduced in v1.4.0
  • Now handles alternative start codons properly to address issue #274
  • Improves multithreading for codon alignment thanks to @nzmacalasdair

v1.4.2

23 Feb 14:54
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  • Addresses bug highlighted in #269. This was introduced in v1.4.0
  • Fixes a problem with genes with overly long names crashing the program

v1.4.1

18 Feb 17:20
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  • Update to ensure gffutils writes to the Panaroo temporary directory rather than the system temporary directory. Previously, this could cause issues when users had strict space requirements on the system tmp directory. It also increased the chance of a collision between temporary files when running multiple instances of Panaroo at the same time.

v1.4.0

13 Feb 21:41
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Includes a number of updates and important bug fixes:

  • New option to only use a random subset of genes for generating a core alignment thanks to @mgalardini
  • New option to only consider valid genes (without stop premature codons and of correct length). Thanks to issue #263 raised by @NickJD
  • Important fix to the panaroo-merge-graph script which had a bug that prevented the --merge-paralogs options from working. This is now the recommended way to run this script.
  • Fixed bug in panaroo-integrate raised by @maxibor
  • added warning if no matching sequences are found between the annotations and the corresponding fasta file/section
  • added check for the number of core genes to prevent a crash if no clusters passed the core frequency threshold

v1.3.4

21 Sep 09:44
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Fixes a number of minor issues:

  • Fixes a bug in the post run alignment script panaroo-msa. This was encountered when not all input genomes were present in the generated pangenome graph.
  • Now prints an informative message if there are no gene clusters that pass the core frequency threshold.
  • Print a more informative error message if an invalid Genbank file is provided.

v1.3.3

11 Apr 10:29
567d6e6
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This release fixes some minor bugs including in

  • panaroo-extract-gene Fixes an issue caused by duplicate gene IDs appearing in separate genomes
  • panaroo-merge Adds a missing parameter that was introduced in the recent release to generate filtered core genome alignments.

v1.3.2

12 Dec 06:32
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This release fixes minor bugs and adds critical new functionality to generate an automatically filtered core genome alignment. We have found that this filtered alignment leads to superior phylogenetic trees.

  • added new core genome alignment output that uses a Block Mapping and Gathering with Entropy (BMGE) filter to remove genes that are likely to cause issues when reconstructing phylogenies.
  • fixed a bug that created many temporary files when using PRANK for gene alignment.
  • fixed a bug in the extract gene post-processing script
  • updated dependencies

v1.3.0

10 Aug 08:57
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This release adds some significant new capabilities to the Panaroo pipeline.

  • adds script to generate (simplified) updated GFF files that include refound gene segments
  • panaroo can now accept seperate GFF and fasta files as well as some genebank file formats
  • fixed bug that led to the merge graph script not cleaning up after itself
  • fixed minor inconsistency in how core genes were defined between summary stats and the alignments generated

v1.2.10

28 Mar 01:20
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  • added script panaroo-extract-gene to extract a fasta file given a gene name
  • fix gene sequence prefilter for non-standard codon tables
  • minor update to simulation script to work with new version of numpy
  • minor fixes to pseudo_full_pangenome and filter_pa scripts