💠Pipeline logic

Pipeline steps

Step	Description	Notes
Read QC	Low-quality bases are trimmed from the ends of each read. After trimming, the read is discarded if fewer than 50% of its bases have a quality score greater or equal to q20, the read is shorter than 32 bp, or the read has 5 or more ambiguous bases. For paired-end data, both read1 and read2 must pass QC filtering for the read pair to be used for analysis. It is assumed that appropriate adapter trimming has already been performed.	Optional
Taxonomic classification	Read classification using the DRAGEN Kmer Classifier	Custom database can be specified
Result filters	User-specified read count threshold [0-1000] applied	Default is 0 or unfiltered
Reporting - Analysis level	XLSX, CSV, HTML, ZIP
Reporting - Sample level	JSON, CSV, HTML, TXT.GZ