FASTQ format options
The fastq_join command combines paired reads into single sequences by
reverse-complementing the reverse read and inserting padding (default NNNNNNNN).
If R1 is the forward read and R2 is the reversed read, the combined read is R1
The forward (R1) read filename is given by the fastq_join
The reverse (R2) read filename is given by the -reverse
The output is written to a FASTQ file by specifying the -fastqout
option and/or to a FASTA file given by -fastaout.
usearch -fastq_join fwd.fastq -reverse rev.fastq -fastaout