Filter reads for hits to the PhiX genome which is used as a spike in Illumina amplicon sequencing.
Input is a FASTA or FASTQ file. A reverse (R2) read file can be specified using -reverse, in which case a read pair is discarded if the forward (R1) and/or reverse (R2) read has a hit to PhiX. If -reverse is specified, -output2 must be specified for the reverse read output file. Output is written in the same format (FASTA or FASTQ) as the input.
Standard output files are supported for reporting PhiX hits.
Multithreading is supported.
usearch -filter_phix reads.fq -output filtered_reads.fq -alnout hits.txt
usearch -filter_phix reads_fwd.fq -reverse reads_rev.fq -output fil_fwd.fq -output2 fil_rev.fq