diff --git a/bin/ExtendOrFormatContigs.pl b/bin/ExtendOrFormatContigs.pl
index eabbb1c..7b278af 100755
--- a/bin/ExtendOrFormatContigs.pl
+++ b/bin/ExtendOrFormatContigs.pl
@@ -1,5 +1,7 @@
   ###############################################################
-  #Marten Boetzer 1-03-2010                                    #
+  #Multi-thread implemented by Jose F. Sanchez-Herrero		#
+  # 1-08-2017							#
+  #Marten Boetzer 1-03-2010                                     #
   #SSPACE perl subscript ExtendOrFormatContigs.pl               #
   #This script, based on the the -x parameter;                  #
   #  -Formats the contigs to appropriate format (-x 0)          #
@@ -9,9 +11,12 @@
   use strict;
   use File::Basename;
   use File::Path;
+  use FindBin qw($Bin);
+  use lib "$Bin/Parallel/";
+  use Parallel::ForkManager;
+  use Cwd qw(abs_path);
 
   my ($MAX, $MAX_TOP, $TRACK_COUNT) = (0, 100, 1);
-
   my $seplines = ("-" x 60)."\n";
 
   my $contig = $ARGV[0];
@@ -37,7 +42,6 @@
   my $filenameOutExt = $base_name . ".singlereads.fasta";
   my ($bin);
   if($extending == 1){
-
     &ExtendContigs($base_name, $filecontig, $filenameOutExt);
     print SUMFILE "\n" if($minContigLength > 0);
     &FormatContigs() if($minContigLength > 0);
@@ -60,63 +64,130 @@ sub ExtendContigs{
   &getUnmappedReads($filecontig, $readfile);
   #-------------------------------------------------CONTIG EXTENSION USING UNMAPPED PAIRS STORED IN $SET
   &printMessage("\n=>".getDate().": Contig extension initiated\n");
-  my $outfileTig =  "intermediate_results/" . $base_name .  ".extendedcontigs.fasta";
 
-  open (TIG, ">$outfileTig") || die "Can't write to $outfileTig -- fatal\n";
   #--------------------------------------------ASSEMBLY START
 
  ASSEMBLY:
-   open(IN, $filecontig) || die "Can't open $filecontig -- fatal\n";
-   my ($exttig_count, $counter, $NCount, $orig_mer, $prevhead) = (0, 0, 0, 0, '');
-   while(<IN>){
-      s/\r\n/\n/;
-      chomp;
-      $seq.= uc($_) if(eof(IN));
-      if (/\>(\S+)/ || eof(IN)){
-         my $head=$1;
-         $orig_mer = length($seq);
-         if($seq ne ''){
-             $NCount++ if($seq=~/([NX])/i);
-             my $start_sequence = uc($seq);
-             my $reads_needed = 1;                        #tracks coverage
-             my $total_bases = $orig_mer * $reads_needed;
-
-             ($seq, $reads_needed, $total_bases) = doExtension("3", $orig_mer, $seq, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $counter, $max_trim) if($orig_mer >= $MIN_READ_LENGTH && $orig_mer >= $min_overlap);
-
-             my $seqrc = reverseComplement($seq);
-             ($seqrc, $reads_needed, $total_bases) = doExtension("5", $orig_mer, $seqrc, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $counter, $max_trim) if($orig_mer >= $MIN_READ_LENGTH && $orig_mer >= $min_overlap);
-
-             my $leng = length($seqrc);
-             my $reversetig = reverseComplement($seqrc);                   ### return to sequence, as inputted
-             if($leng > $orig_mer){ ### commented out: && $start_sequence ne $seqrc && $start_sequence ne $reversetig
-               my $cov =  $total_bases / $leng;
-               printf TIG ">extcontig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $leng, $reads_needed, $cov, $reversetig);    #print contigs to file
-               $exttig_count++;
-             }else{
-               my $cov = $reads_needed = 0;
-               my $singlet_leng = length($start_sequence);
-               printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $leng, $reads_needed, $cov, $reversetig);    #print singlets to file
-             }
-         }
-         CounterPrint(++$counter);
-         $prevhead = $head;
-         $seq='';
-      }else{
-         $seq .= uc($_);
-      }
-   }
-  CounterPrint("                ");
-  print SUMFILE "\tNumber of contig sequences =".($counter-1). "\n";
-  print SUMFILE "\t\tNumber of contigs containing N's (may prevent proper contig extension) = $NCount\n";
-
-  print SUMFILE "\tNumber of contigs extended = $exttig_count\n".$seplines;
-  close IN;
-  $filecontig = $outfileTig;
-  if($@){
-     my $message = $@;
-     &printMessage("\nSomething went wrong running $0 ".getDate()."\n$message\n");
-  }
-  close TIG;
+ 
+ ## Split given fasta file in as many CPUs as expected and send multiple threads for each
+ 	# Splits fasta file and takes into account to add the whole sequence if it is broken
+	my $file = $filecontig;
+	my $file_size = -s $file; #To get only size
+	my $block = int($file_size/$threads);
+	
+	my $path = abs_path();
+
+	open (FH, "<$file") or die "Could not open source file. $!";
+	print "\t- Splitting file into blocks of $block characters aprox ...\n";
+	my $j = 0; my @files;
+	my @name = split("/", $file);
+	my $file_name = $name[-1];
+	while (1) {
+		my $chunk;
+		my @tmp = split ("\.fasta", $file_name);
+		my $block_file = $path."/intermediate_results/".$tmp[0]."_part-".$j."_tmp.fasta";
+		push (@files, $block_file);
+		open(OUT, ">$block_file") or die "Could not open destination file";
+		if (!eof(FH)) { read(FH, $chunk,$block);  
+			if ($j > 0) { $chunk = ">".$chunk; }
+			print OUT $chunk;
+		} ## Print the amount of chars	
+		if (!eof(FH)) { $chunk = <FH>; print OUT $chunk; } ## print the whole line if it is broken	
+		if (!eof(FH)) { 
+			$/ = ">"; ## Telling perl where a new line starts
+			$chunk = <FH>; chop $chunk; print OUT $chunk; 
+			$/ = "\n";
+		} ## print the sequence if it is broken
+		$j++; close(OUT); last if eof(FH);
+	}
+	close(FH);
+
+	my $pm =  new Parallel::ForkManager($threads); ## Number of subprocesses not equal to CPUs. Each subprocesses will have multiple CPUs if available
+	$pm->run_on_finish( 
+	sub { my ($pid, $exit_code, $ident) = @_; 
+		print "\n\n** Child process finished with PID $pid and exit code: $exit_code\n\n"; 
+	} );
+	$pm->run_on_start( sub { my ($pid,$ident)=@_; print "\n\n** Parsing block of FASTA file $ident PID:$pid\n\n"; } );
+	for (my $i=0; $i < scalar @files; $i++) {
+		my $pid = $pm->start($files[$i], $i) and next; print "\nExecuting subprocess command\n\n";
+		## Send subprocess
+
+	   	open(IN, $files[$i]) || die "Can't open $files[$i] -- fatal\n";
+	
+		my $out_put = $files[$i]."-extendedcontigs.fasta";
+		open (OUT, ">$out_put");
+	   	my ($exttig_count, $counter, $NCount, $orig_mer, $prevhead) = (0, 0, 0, 0, '');
+		$/ = ">"; ## Telling perl where a new line starts
+		while (<IN>) {		
+			next if /^#/ || /^\s*$/;
+			chomp;
+			my ($head, $seq) = split(/\n/,$_,2);
+			next unless ($head && $seq);
+		
+			$NCount++ if($seq=~/([NX])/i);
+			my $start_sequence = uc($seq);
+			my $reads_needed = 1;                        #tracks coverage
+			my $total_bases = $orig_mer * $reads_needed;
+		
+			($seq, $reads_needed, $total_bases) = doExtension("3", $orig_mer, $seq, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $counter, $max_trim) if($orig_mer >= $MIN_READ_LENGTH && $orig_mer >= $min_overlap);
+		
+			my $seqrc = reverseComplement($seq);
+			($seqrc, $reads_needed, $total_bases) = doExtension("5", $orig_mer, $seqrc, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $counter, $max_trim) if($orig_mer >= $MIN_READ_LENGTH && $orig_mer >= $min_overlap);
+		
+			my $leng = length($seqrc);
+			my $reversetig = reverseComplement($seqrc);                   ### return to sequence, as inputted
+			if($leng > $orig_mer){ ### commented out: && $start_sequence ne $seqrc && $start_sequence ne $reversetig
+			  my $cov =  $total_bases / $leng;
+			  printf OUT ">extcontig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $leng, $reads_needed, $cov, $reversetig);    #print contigs to file
+			  $exttig_count++;
+			}else{
+			  my $cov = $reads_needed = 0;
+			  my $singlet_leng = length($start_sequence);
+			  printf OUT ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $leng, $reads_needed, $cov, $reversetig);    #print singlets to file
+			}
+			$counter++;
+		}
+		$/ = "\n";
+		close(IN); close (OUT);
+
+		## print STATS
+		my $stats = $files[$i]."-extendedcontigs.STATS.txt";
+		open (STATS, ">$stats");
+		print STATS "NCount=$NCount\ncounter=$counter\nexttig_count=$exttig_count\n";
+		close (STATS);
+		
+		## finish subprocess
+		$pm->finish($i); # pass an exit code to finish
+	}
+	$pm->wait_all_children; print "\n** All parsing child processes have finished...\n\n";
+
+ 	## concatenate results
+  	my $outfileTig =  $path."/intermediate_results/" . $base_name .  ".extendedcontigs.fasta";
+  	my $stats_file = $path."/intermediate_results/stats-tmp.txt";
+  	
+  	#open (TIG, ">$outfileTig") || die "Can't write to $outfileTig -- fatal\n";
+	system("cat $path/intermediate_results/*extendedcontigs.fasta >> $outfileTig");
+	system("cat $path/intermediate_results/*extendedcontigs.STATS.txt >> $stats_file");
+	
+	my %stats;
+	open (STAT, "<$stats_file");
+	while (<STAT>) {
+		my $line = $_;
+		chomp $line;
+		my @array = split("=", $line);
+		$stats{$array[0]} += $array[1];
+	}
+	close (STAT);
+
+ 	print SUMFILE "\tNumber of contig sequences =".($stats{"counter"}-1). "\n";
+  	print SUMFILE "\t\tNumber of contigs containing N's (may prevent proper contig extension) = ".$stats{"NCount"}."\n";
+  	print SUMFILE "\tNumber of contigs extended = ".$stats{"exttig_count"}."\n".$seplines;
+
+  	$filecontig = $outfileTig;
+  	if($@){
+     	my $message = $@;
+     	&printMessage("\nSomething went wrong running $0 ".getDate()."\n$message\n");
+  	}  
 }
 
 ###STORE CONTIGS TO APPROPRIATE FORMAT WHEN CONTIGS WILL NOT BE EXTENDED