Removing repeated reads from nanopore 1D² reads
You can exclude the 1D² reads by generate a list of the ids from the 1D² reads, then filtering those reads out from the 1D fastq files. Here's one way to do that using some accessory scripts that I have written:

$ cat 1d2_reads.fq | ~/scripts/fastx-length.pl | awk '{print $2}' &gt; readNames.txt
$ cat 1d_reads.fq | ~/scripts/fastx-fetch.pl -v -i readNames.txt &gt; filtered_1d_reads.fq


In order to deal with the concatenated read IDs, it's necessary to switch to a language like Perl that supports the use of backreferences for the splitting. The following perl command (replacing the first line in the above procedure) inserts a line break after the 36th character in the 2nd value, then prints that value:

$ cat 1d2_reads.fq | ~/scripts/fastx-length.pl | perl -lane '$F[1] =~ s/(.{36})/$1\n/; print $F[1];' &gt; readNames.txt


So a full sequence of operations would look something like this:

$ cat 1d2_reads.fq | ~/scripts/fastx-length.pl | perl -lane '$F[1] =~ s/(.{36})/$1\n/; print $F[1];' &gt; readNames.txt
$ cat 1d_reads.fq | ~/scripts/fastx-fetch.pl -v -i readNames.txt &gt; filtered_1d_reads.fq
$ cat 1d2_reads.fq filtered_1d_reads.fq &gt; unique_reads.fq