For FASTQ sequencing data: organise raw data, check quality, filter, prepare for alignment and summarise everything in a MultiQC report.
Organise FASTQ files, the sample information sheet and sequencing batch information by sample ID.
Sample names must match the metadata exactly.
Check base quality, adapter contamination, GC content, duplicated sequences and read length distribution.
Don't just look at pass/fail; understand what each warning means.
Remove adapters, low-quality reads and overly short sequences to produce cleaned data.
Record filtering parameters in the methods section.
Combine FastQC and filtering results from multiple samples into a single report.
MultiQC reports are good for spotting anomalous samples quickly.
Move on to alignment, quantification, variant calling or microbiome analysis depending on the research goals.
Don't rush into downstream analysis if QC results are not acceptable.
