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Old 11-30-2010, 08:36 PM   #1
ljhwahaha
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Location: China

Join Date: Oct 2010
Posts: 3
Default Need some suggestion for overlap assembler

Recently, i faced with a problem, I want to overlap the sequences in order to have a longer one, but i can't find out a assembler which could be suitable to my data.
The length of my data is wide range, from 102bp to 87249bp, with N50 length of 738bp, so it count not be assembled using 454 data assembler, such as Newbler.
What's more, the total bases number of my data is about 1.9G, so it seems to be impossible to use Sanger data assembler.
What i want to do is to extend the sequences based on the overlap relationship between them, if someone have any suggestion, please inform me.
thank you
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Old 11-28-2012, 10:00 AM   #2
niazi84@hotmail.com
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Location: Uppsala

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Default

hello,

I also want to do the same but could not find any software. Did you find any overlaping assembler?
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Old 11-29-2012, 04:39 AM   #3
sklages
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Have a look at Celera Assembler, http://sourceforge.net/apps/mediawik...itle=Main_Page
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Old 03-19-2014, 04:02 AM   #4
amaurizio
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Location: Italy

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Hello,
I used Pear to merge my Illumina (MiSeq sequencer) pair-end reads.
I'd like to know the overlap length in each of the merged reads in order to calculate min length, max, average, mode, median etc...
Can you suggest my how to do?
I tried with a perl script (length R1 + length R2 - length MergedR1R2) but I am not very good in programming....
Can anybody help me and tell me how to do this?
Thanks!!
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Old 03-24-2014, 06:11 AM   #5
krobison
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Location: Boston area

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Code:
#!/usr/bin/perl
#!/usr/bin/perl
# debugging left as exercise for student :-)
use strict;

foreach my $arg(@ARGV)
{
   my %lengths=();
   # read sequence file for lengths
   my $rdr=new Bio::SeqIO(-file=>$arg,-format=>'fastq');
   my $sum=0; my $cnt=0;
   while (my $rec=$rdr->next_seq)
   {
      $lengths{$rec->length}++; $sum+=$rec->length; $cnt++;
   }
   my @sortedLengths=sort {$a<=>$b} keys %lengths;
   my $minLen=$sortedLengths[0];
   my $maxLen=$sortedLengths[$#sortedLengths];
   my $meanLen=$sum/$cnt;
   my ($modeLen)=sort {$lengths{$b}<=>$lengths{$a}} keys %lengths;

   my $medLen="error";
   # calculating median left as exercise

   print join("\t",$arg,$minLen,$maxLen,$meanLen,$modeLen,$medLen),"\n";
}
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Old 03-25-2014, 08:27 AM   #6
amaurizio
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Thank you very much!
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