qc: raw data
Workflow for QC of raw files before any other processing steps:
- get general statistics from FASTQ files, e.g. number of reads, quality profiles etc.
- compare samples, especially those with multiple sequencing runs
-
MultiQC summary from FastQC reports -
Sample similarity ( mash
)
Note: not usingsourmash
for sample similarity as k-mer trimming/filtering with khmer
takes too long