How to check for phi_x phiX reads with Wochenende

[colindaven]

Illumina often has phiX DNA spiked in, but most reads are removed by the bcl2fastq program which generates fastq. See OpenGene/fastp#225

You can use this reference (available on request) to check phiX contamination. Important for de novo assembly read preprocessing, or when you use single (i7 only) not double (i7 and i5) Illumina adapters.

Ref:
refSeqs_allKingdoms_201910_3_with_UniVec.fasta.gz

Sequence:
gnl_uv_J02482_1_1_5386_49_Coliphage_phi_X174