Version Compatibility

Reference examples tested with: BBTools 39.0+, Bowtie2 2.5.3+, FastQ Screen 0.15+, FastQC 0.12+, MultiQC 1.21+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Contamination Screening

Screen FASTQ files against multiple genomes to identify contamination sources using FastQ Screen.

"Check for contamination in sequencing data" → Align a sample of reads against multiple reference genomes to identify cross-species or cross-sample contamination.

• CLI: fastq_screen --conf fastq_screen.conf reads.fq

FastQ Screen Overview