Quality is assessed before any preprocessing. The most important graph is the
FastQC: Status Checks.
As with a stop light, green boxes reflects high quality data, yellow reflects a warning, and red reflects concern. Thresholds for this graph are custom tailored to your sequencing platform and experimental design. For example, nanopore sequences will flag as a warning if the average
Per Sequence Quality (measured in Phred score) is below Q8, whereas Illumina sequences will flag if below Q20.
For a full description of graph content, please see the FastQC manual.
Basic assembly statistics, such as N50 and total length, are calculated with QUAST. We refer the reader to the QUAST interpretation guide for details on assembly plots and statistics in the BugSeq per-sample reports.