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Some bioinformatic programs don't like long contig/scaffold names. Plus long names are ugly, time consuming to scan and just take up space.

So, before you do anything with the genome assembly you should consider changing the names of the contigs/scaffolds to something sensibly short like scaffold_1, scaffold_2

<code>
#!/usr/bin/perl

#numbers contigs sequentially

$num=1;
	open (FI,"name_of_genome_assembly.fasta");
		while (<FI>)
			{
			$fline=$_;
    			chomp($fline);
    			if ($fline =~/>/)
    			{
    			print ">contig_".$num."\n"; #if they are scaffolds then change contig to scaffold
    			$num=$num+1;
    			}
    			else
    			{
    			print "$fline\n";
    			}	
    		}
    	close FI;
 </code>
   
 To run this program copy the code into a text file and save as something like **changenames.pl**
 When you save this file make sure you save it with unix line breaks not mac or windows line breaks.
 Make sure you have replaced **name_of_genome_assembly.fasta** with the name of the file you want to change.
 Make the file changenames.pl executable by 
  chmod 777 changenames.pl
Then run it by
  ./changenames.pl > name_of_new_file.fasta
  
 Some people may want to preserve information in the original header line. For example
Consensus_Consensus_Consensus_linear_0_len:1351806_cov:56_len:1352678_cov:61 is a really long name that will cause
you trouble down the road but maybe you want to preserve the text information 1351806

<code>
#!/usr/bin/perl

#preserve some bits of information in the header

open (FI,"name_of_genome_assembly.fasta");
		while (<FI>)
			{
			$fline=$_;
    			chomp($fline);
    			if ($fline =~/>/)
    			{
    			
    			$fline =~/len:([0-9]+)/; 
    			$info=$1;
    			print ">contig_".$info."\n"; #if they are scaffolds then change contig to scaffold
    			
    			}
    			else
    			{
    			print "$fline\n";
    			}	
    		}
    	close FI;
  </code>
 
If the changes are more complicated than this talk to someone who knows perl or as a last, desperate resort someone who codes in python or some other woefully inadequate programming language.

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