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Old 11-26-2012, 06:28 PM   #1
ndeshpan
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Exclamation Sspace scaffolder : does it take the "insert size" or the "fragment size"

Hi all,

I am trying to use SSpace for scaffolding my already assembled contigs:

I wanted to know if the insert size column in the library.txt file for SSpace is the "insert size" exclusive of the read length or infact the fragment size (with the read length),

cheers,

Nandan
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Old 11-28-2012, 02:18 AM   #2
boetsie
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Hi Nandan,

sorry I missed your post yesterday. The insert size in SSPACE is referred as the fragment size, so including the read length.

Regards,
Boetsie
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Old 11-28-2012, 01:11 PM   #3
ndeshpan
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Thanks Boetsie..this solves my confusion :-)

cheers,

nandan
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Old 11-28-2012, 09:25 PM   #4
ndeshpan
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Hi Boetsie,

One more quick question..

I am trying to use Hawkeye visualisation for displaying my "Scaffolds/contigs/reads" in tandem..

1) I have used velvet for assembly and created a ".afg" file. (1 paired-end library)

2) I have then used Space with the same set of paired-end reads to scaffold the contigs.

Is there a way you can suggest to provide the scaffold relationship to Hawkeye in addition to the contig information in .afg file form velvet?

appreciate your help,

cheers,

Nandan
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Old 11-29-2012, 07:12 AM   #5
boetsie
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Hi Nandan,

I'm sorry, but I've never used the Hawkeye software, so I can't comment on that. Maybe someone else can help you with this? For example the developers of Hawkeye?

Regards,
Boetsie
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Old 11-29-2012, 01:43 PM   #6
ndeshpan
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Hi Boetsie,

No worries..thanks .. I will check if anyone else has any suggestion and also get back to Hawkeye developers,,

cheers,

Nandan
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Old 11-29-2012, 06:10 PM   #7
AnthonyB
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I've also been dealing with the problem of getting the scaffolds of SSPACE displayed in Hawkeye for assessment of assembly quality.

From my investigations, it seems that you have to parse the output of the SSPACE evidence file into a series of scaffold (SCF) and supporting contig edge (CTE) records for inclusion in the AMOS afg file that you load into Hawkeye.

I'm working on a script that will hopefully accomplish this, but it's still early days. If I get it ironed out, I'll be happy to share it.

Cheers,

Anthony
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Old 11-29-2012, 06:15 PM   #8
ndeshpan
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Hi Anthony,

thanks for your response.. I will appreciate if u can share the script when you are ready with it.. I will also work from my end to check if I can get any solution ..now that there does not seem to be a readily available script/tool,

cheers,

Nandan
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Old 12-06-2012, 03:36 PM   #9
ndeshpan
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Hi Boetsie,

I have a question about a specific parameter in Sspace:

I am using SSPACE-BASIC-2.0_linux-x86_64

The ‘–m’ minimum overlap
---------------
Minimum number of overlapping bases of the reads with the contig
during overhang consensus build up. Higher ‘-m’ values lead to more
accurate contigs at the cost of decreased contiguity. We suggest to take
a value close to the largest read length. For example, for a library with
36bp reads, we suggest to use a -m value between 32 and 35 for reliable contig extension.

Since I am using a library from illumina with a read length 102, I was trying to use m=90 but I could see from the error report that the maximum allowable value of m=50.

How do I get over this problem? Appreciate your assistance.

cheers,

nandan
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Old 12-10-2012, 06:50 AM   #10
boetsie
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Hi Nandan,

You could get a work-around for this by removing the number in the SSPACE main file (SSPACE_Basic_v2.0.pl). Please change this line in the code;

die "ERROR: -m must be a number between 15-50. Your inserted -m is $min_overlap ...Exiting.\n" if(!($min_overlap =~ /^\d+$/) || $min_overlap < 10 || $min_overlap > 50);

Set the '> 50' to your liking.

Regards,
Boetsie

Quote:
Originally Posted by ndeshpan View Post
Hi Boetsie,

I have a question about a specific parameter in Sspace:

I am using SSPACE-BASIC-2.0_linux-x86_64

The m minimum overlap
---------------
Minimum number of overlapping bases of the reads with the contig
during overhang consensus build up. Higher -m values lead to more
accurate contigs at the cost of decreased contiguity. We suggest to take
a value close to the largest read length. For example, for a library with
36bp reads, we suggest to use a -m value between 32 and 35 for reliable contig extension.

Since I am using a library from illumina with a read length 102, I was trying to use m=90 but I could see from the error report that the maximum allowable value of m=50.

How do I get over this problem? Appreciate your assistance.

cheers,

nandan
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Old 12-10-2012, 01:28 PM   #11
ndeshpan
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Thanks Boetsie..Appreciate your help.

cheers,

Nandan
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Old 02-15-2015, 08:41 PM   #12
salwani
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Hi Boetsie,

I want to use SSPACE to scaffolds my assembly. I did hybrid assembly using Cerulean with Illumina HiSeq and PacBio. However, I don't know where can I get the standard deviation for the reads. I want to scaffold my assembly using Illumina reads. According to the NGS report that I got from the sequencing company, the insert size for my illumina reads is 500bp and the reads length is 90bp. So the number of my fragment size should be 590bp. Is there any software that I can use to get the standard deviation of the reads?

Thank you.
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Old 02-15-2015, 08:53 PM   #13
salwani
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Default standard deviation-libraries SSPACE

Hi Boetsie,

I want to use SSPACE to scaffolds my assembly. I did hybrid assembly using Cerulean with Illumina HiSeq and PacBio. However, I don't know where can I get the standard deviation for the reads. I want to scaffold my assembly using Illumina reads. According to the NGS report that I got from the sequencing company, the insert size for my illumina reads is 500bp and the reads length is 90bp. So the number of my fragment size should be 590bp. Is there any software that I can use to get the standard deviation of the reads?

Thank you.
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Old 02-15-2015, 11:17 PM   #14
sarvidsson
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Align the reads to your contigs and run Picard's CollectInsertSizeMetrics: http://broadinstitute.github.io/pica...ertSizeMetrics
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