ggCaller v1.4.1

• Implements iterative gene calling, allowing genes to be called in first pass, and new genomes to be called against the original set
• Reimplements gene clustering algorithm to enable iterative clustering, removing multiple passes through clusters with a single greedy pass
• Adds '--gene-finding-only' option to output gff3 files compatible with Panaroo input
• Adds intermediate file writing to reduce memory consumption
• Replace '--data' with '--prev-run' option to allow for iterative updates of gene calls when analysing new genomes
• Updates unitig annotation pipeline to function with new iterative functionality
• Updates documentation with changes to iterative gene calling

ggCaller v1.3.7

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

Minor updates to v1.3.5:

• Corrects deprecation warning with Biopython v1.80

ggCaller v1.3.5

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

Minor updates to v1.3.3:

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

ggCaller v1.3.3

Minor updates to v1.3.2:

• Fixes issue with linking of torch library.

ggCaller v1.3.2

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

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

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

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.