how to order paired-end reads to use in kaiju?

Question

[Gabriel]

I am trying to use kaiju for a taxonomic analysis and when trying to use the .fastq files resulting from the process with Trimmomatic, I get an error because the sequences of reads are not in the same order in files_1.fastq and files_2.fastq (as described on github for kaiju is a requirement). Could someone guide me on how to deal with this situation?

Thank you very much in advance

[shenwei356]

• match up paired-end reads from two fastq files with seqkit,
• or match up paired end fastq files quickly and efficiently with fastq-pair,

[GenoMax]

repair.sh from BBMap sute to add another tool: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/repair-guide/