The following preserves output order if desired. Here, the chunk_id value is used for ensuring ordered entry into the @found array. It is important for workers to gather even though sending an empty @results. The reason is that the Manager process must know that a given chunk_id has completed.

use strict;
use warnings;

use MCE::Loop;
use MCE::Candy;

my @patterns = ( "biopattern1", "biopattern2", "biopattern3" );
my $search   = join('|', @patterns);
my $regex    = qr/$search/;

open my $fh, "gunzip -c in.fastq.gz |" or die "open error: $!";

my @found;

MCE::Loop->init(
    max_workers => 4,
    chunk_size => 50,
    RS => "\n@",
    gather => MCE::Candy::out_iter_array(\@found)
);

MCE::Loop->run( sub {
    my ( $mce, $chunk_ref, $chunk_id ) = @_;
    my @results;

    for my $i ( 0 .. $#{ $chunk_ref } ) {
        if ( $chunk_ref->[$i] =~ /$regex/ ) {
            push @results, $chunk_ref->[$i];
        }
    }

    MCE->gather( $chunk_id, @results );

}, $fh );

MCE::Loop->finish();

close $fh;

print join('', @found);
[download]