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Releases: bacpop/ggCaller

ggCaller v1.3.7

18 Jul 08:31
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Minor updates to v1.3.6:

  • Corrects out of range error during contig mapping due to 'empty' contig as in issue #35

ggCaller v1.3.6

05 Jun 10:02
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Minor updates to v1.3.5:

  • Corrects deprecation warning with Biopython v1.80

ggCaller v1.3.5

31 May 09:50
ebcdd26
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Minor updates to v1.3.4:

  • Corrects issue with generating core genome alignment with pan option
  • Converts FM-index to uppercase to avoid indexing issues and GFF generation
  • Adds docker build continuous integration
  • Corrects installation check issue with latest version of HMMER 3.4
  • Adds manual download and specification of ggCallerdb (BALROG and annotation databases)

ggCaller v1.3.4

28 May 11:30
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Minor updates to v1.3.3:

  • Corrects issue with over-clustering during mistranslation correction.
  • Sets default annotation to "fast"

ggCaller v1.3.3

17 Jan 15:29
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Minor updates to v1.3.2:

  • Fixes issue with linking of torch library.

ggCaller v1.3.2

07 Jan 12:53
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Minor updates to v1.3.1:

  • Addresses bug where core genome alignment fails if one sequence has no core genes.
  • Changes naming of alignment files from gene name to centroid name for ease of parsing.

ggCaller v1.3.1

15 Dec 14:53
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Minor updates to v1.3.0:

  • Adds start-site kmer-ization to improve sensitivity of matches across colours.
  • Adds start-site score tolerance to check shorter ORFs with certain probability or greater of being real (based on stop-codon coverage).
  • Bug fixes.

ggCaller v1.3.0

15 Dec 14:52
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Major updates to v1.2.4:

  • Significant upgrades to memory and time efficiency.
  • Replaces seqan3 with sdsl v3 for fm-indexing.
  • Implements panaroo for gene-call correction and pangenome analysis.
  • Adds cluster-based annotation using diamond and hmmer.
  • Adds GFF, gene presence/absence and structural variant presence/absence outputs.
  • Adds gene frequency and rarefaction curve plots.
  • Implements core and pangenome alignment using mafft.
  • Adds pangenome reference generation.
  • Implements neighbouring joining tree generation using rapidnj.
  • Implements within-cluster SNP-calling using SNP-sites.
  • Implements graph-querying.

ggCaller v1.2.4

23 Jun 16:22
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Major updates to v1.2.3:

  • Significantly improves memory consumption and run-time by implementing iterative graph traversal.
  • Implements pointers to avoid copying of graph and BALROG model objects during multiprocessing.

ggCaller v1.2.3

24 Apr 11:19
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Minor updates to v1.2.2:

  • Reduces memory overhead through per-genome multithreading and removal of string processing.
  • Removes amino acid kmer filter in Balrog gene scoring, significantly reducing memory overhead with negligible affect on call precision.

Bug fixes:

  • Fixes issue with negative cycle errors during gene scoring.