my $NUM_THREADS = 5;
my $BUFFER_SIZE = 1;

my @inQueues = ();
my @threads  = ();
my $outQ     = Thread::Queue->new();
my $readyQ   = Thread::Queue->new();

# create worker threads
for ( my $i = 0; $i < $NUM_THREADS; $i++ )
{
    my $inQ  = Thread::Queue->new();
    my $thr  = threads->create( sub {
        # see the Worker Threads section for this
        ...
    } );
    
    push @inQueues, $inQ;
    push @threads,  $thr;
    
    # start the threads
    $readyQ->enqueue( $i );
}

# create writer thread
my $curLot   = 0;
my $curBatch = 0;
my $curPart  = 0;

my $writerThr = threads->create( sub {
    # see the Writer Thread section for this
    ...
} );

# give a line from SEED_FILE to each thread
for ( ;; )
{
    last if eof( $SEED_FILE );

    my $nextThread = $readyQ->dequeue();
    
    chomp( my $fastaComment = <$SEED_FILE> );
    chomp( my $readSequence = <$SEED_FILE> );      
    
    my %item = ( 'lot'   => $curLot,
                 'batch' => $curBatch,
                 'part'  => $curPart,
                 'fasta' => $fastaComment,
                 'read'  => $readSequence, );

    $inQueues[ $nextThread ]->enqueue( \%item );

    # get the next batch/part number
    $curPart = ($curPart + 1) % $NUM_THREADS;
    if ( $curPart == 0 ) { ++$curBatch; $curBatch %= $BUFFER_SIZE; }
    if ( $curPart == 0 && $curBatch == 0 ) { ++$curLot; }
}

# let threads know that input is done
for ( my $i = 0; $i < $NUM_THREADS; $i++ )
{
    $inQueues[ $i ]->enqueue( undef );
}

# wait for threads to finish
foreach my $thr ( @threads )
{
    $thr->join();
}

$writerThr->join();