merging paired-end reads

For input directories that contain paired FASTQ files that need to be merged prior to processing, passing the --merge (-m) flag instructs abstar to merge paired files with fastp:

abstar run --merge path/to/input/ path/to/output/

Reads will be merged prior to annotation, and the merged reads will be deposited into a merged sub-directory located within the output directory. abstar can also accomodate interleaved FASTQ files, in which paired-end reads are stored in a single file. This is common when using data downloaded from the SRA. To process interleaved FASTQ files, pass the --interleaved_fastq flag:

abstar run --interleaved_fastq path/to/input/ path/to/output/

Note

The --interleaved_fastq flag will automatically trigger read merging, so the --merge flag is not necessary.