Version 2.2.3

Fixes a bug in rare cases when running ariba summary (was dying with error ariba.summary_cluster_variant.Error: Mismatch in number of inferred nucleotides ...)

Version 2.2.2

Fixes a few bugs relating to contig names and renaming. Now replaces any of the following with an underscore: | ( ) [ ] ; " ' : ! @ , -

Version 2.2.1

Fixes aln2meta that was broken from last release.

Version 2.2.0

Changes:

• summary variant reporting options simplified
• summary phandango colours tweaked (NAs are now white)
• summary reports "interrupted" in the assembled column for full length genes that have stop codon/frameshift mutations
• add SRST2's version of argannot to getref
• add VFDB full to getref, so can now choose between vfdb_core and vfdb_full
• add option --all_coding to preparef. Gives an alternative to suppling a metadata tsv file
• add option --only_cluster to summary to pull out one cluster

Bug fixes:

• can handle whitespace in FASTA headers
• various small fixes in summary output (particularly for variants)
• report column ref_base_assembled sometimes incorrectly reported the ref length

Version 2.1.0

Changes:

• report het snps for noncoding sequences
• add plasmidfinder
• write all assemblies to a single file at the end
• better naming of clusters when using argannot

Bug fixes:

• off by one error in ref and contig positions of variants in some report lines
• samtools/bcftools parameters changed for snp calling. Diploid assumption was making some Q scores zero, so got filtered out when they shouldn't have
• cluster naming fixed (was getting broken by vfdb)
• catch when no proper pairs mapped and nothing gets assembled. Writes empty report instead of crashing.

Version 2.0.0

Significant methods, run time, and quality of results improvements over previous version.

• not backwards compatible. File formats have changed
• reference sequences can be noncoding or genes, and presence/absence or variants only
• initial mapping to allocate reads to clusters with minimap and cd-hit-est-2d instead of bowtie2
• better cluster naming
• assembly with fermi-lite instead of spades+sspace+gapfiller (assemblies are so small that sspace and gapfiller were not doing anything anyway)
• find nearest reference sequences using MASH
• rough tree for Phandango made using dendropy, removing the dependency on R and its ape package

Version 1.0.1

Bug fix: sometimes false-positives called, when whole gene apparently assembled, but it should not have been. Caused by using spades --untrusted-contigs option. Now --untrusted-contigs option is not used.

Version 1.0.0

Major improvements since the previous version

• Not backwards compatible. File formats have changed.
• Can download and use data from CARD, Resfinder, Argannot and VFDB
• Better handling of variants
• Support non-coding sequences in addition to genes
• More readable summary files and better Phandango output
• Multithreading
• Numerous methods improvements and bug fixes

Version 0.6.0

• New flag has_nonsynonymous_variants
• summary output number 3 now split into two numbers 3 or 4: 3=gene present in a unique contig that has at least one non-synonymous variant. 4=as 3, but no non-synonymous variants
• option to output all samples when running summary, ie do not remove rows/columns that are all zeros (ariba summary --no_filter)

Version 0.5.0

• Handle the case when no reads map to any of the reference genes
• Make nicely formatted fasta file of reference genes to stop tools dying
• Write fasta files of assembled gene sequences for each cluster
• bug fix: refcheck now dies if there are spaces in any sequence name