Regarding first point:

 1. for FILE in $(ls *_R1.fastq | sed 's/_R1.fastq//') -- list all the files endings with `_R1.fastq` (ls *_R1.fastq) and remove the end string `_R1.fastq`  for all the listed files
 2. within loop, `${FILE}_R1.fastq ${FILE}_R2.fastq`  -- reconstruct R1 and R2 fastq.

Regarding second point:

$ parallel --dry-run 'kraken2 --db path/plant_db --memory-mapping --threads 8 --use-mpa-style --confidence 0.1 --report path/{=s/_R1.fastq//=}_report.txt --paired {} {=s/_R1.fastq//=}_R2.fastq --report-zero-counts --output path/{=s/_R1.fastq//=}_taxa.txt' ::: *_R1.fastq

Execute in the same directory where R1 and R2 are located. Parallel is a dry-run. Remove dry-run when you are okay with output commands. When you do not understand a loop, please use echo. While using parallel, you let either parallel handle threads (-j2) or program let handle threads (--threads 2).

The sed argument 's/_R1.fastq//' has 3 parts. Each is separated by /.

• s means substitution
• _R1.fastq is something to be substituted
• The next is actually empty, i.e., substitute _R1.fastq with nothing.

So when ls generate a list of files with _R1.fastq at the end, sed will remove the _R1.fastq in each file. FILE becomes the prefixes of *_R1.fastq.

You can try to see what the FILE will be by echo $(ls *_R1.fastq | sed 's/_R1.fastq//').