Release 0.2.0

IRIDA Line-List Metadata

• For each gene in the 'gene screening file', both the 'detection status' (True/False) and the detected allele
  are written to the IRIDA line-list. Alleles are also reported in the 'gene_detection_status.tsv' output file.

Parameters

• Limited pipeline parameters to simplify and standardize operation
  • Resistance Gene Database is fixed on CARD database.
  • Cannot disable post-assembly correction or read trimming.
  • Cannot change contig name format
  • Cannot provide 'extra spades options' to shovill assembler
• Added thresholds for resistance gene %Coverage and %Identity during secondary screening phase

Output

• The gene screening file used for the analysis is included in the pipeline output