1.3.0

Preliminary implementation for AMR/VFG annotation.

Use --amr option to enable it.
Please see https://github.com/nigyta/dfast_core/?tab=readme-ov-file#experimental-work for more details.

• blastn should be placed in your PATH
• PlasmidFinder is required. Please install it following the instruction at genomicepidemiology/plasmidfinder

1.2.18

fix_partial_CDS function implemented

Fix pseudo-partial CDS predicted at the end of the contig, but is likely to be intact.
The one that meet the following conditions will be retained as a misc_feature or a intact CDS.

• Starts at the coordinate 1 (+ strand) or at the end of contig (- strand)
• 5'-end is missing and 3'-end is intact (+ strand) or the opposite case (- strand)
• length is multiple of 3 and > min_length
• the CDS has significant protein hit

For CDS on + strand, partial_flag 10, strand +, len>=500
For CDS on - strand partial_flag 01, strand -, len>=500

if the first 3 nuleotides are in [ATG, GTG, TTG], the CDS is fixed as intact. Otherwise, it is annotated as misc_feature.

1.2.15

• Added output for the summary of pseudogene detection
• Fixed bug in PseudogeneDetection when transl_except is found in the fragmented contig.
  transl_except will be ignored when insertion/deletion/stop_cond is found in the same alignment.
• Fixed bug in automatic DB indexing when .pal file exists

1.2.12

dfast_file_downloader.py updated (http download from NCBI)

v.1.2.6: Added options to enable GeneMarkS2, Diamond, RNAmmer

Added options to enable GeneMarkS2, Diamond, RNAmmer
As per the pull request #25 and the issue #20, command-line options to enable GeneMarkS2, Diamond, RNAmmer have been added.
See FAQ for more details.

  --aligner STR         Aligner to use [ghostx(=default)|blastp|diamond]
  --use_genemarks2 STR  Use GeneMarkS2 to predict CDS instead of MGA. [auto|bact|arch]
  --use_rnammer STR     Use RNAmmer to predict rRNA instead of Barrnap. [bact|arch]

Note that GeneMarkS2, Diamond, RNAmmer are not bundled in the software package. If you want to use them, please install them by yourself.

Thank @AaronRuben for the PR for GeneMarkS2!