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Old 05-18-2015, 02:41 AM   #1
amitbik
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Location: Europe

Join Date: May 2013
Posts: 53
Default SSPACE scaffolding

Hi All,

I am using SSPACE for scaffolding. After running sspace i am getting same no of scaffolds as the no of contigs i got but the no of scaffold should be less then the no of contig. Am i correct?

Here is my command

perl SSPACE_Standard_v3.0.pl -l libraries.txt -s contigs.fa -T 4 -b out

The summary file

READING READS lib1:
------------------------------------------------------------
Total inserted pairs = 2880237
------------------------------------------------------------



LIBRARY lib1 STATS:
################################################################################

MAPPING READS TO CONTIGS:
------------------------------------------------------------
Number of single reads found on contigs = 209
Number of read-pairs used for pairing contigs / total pairs = 33 / 33
------------------------------------------------------------

READ PAIRS STATS:
Assembled pairs: 33 (66 sequences)
Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3000 +/-750): 0
Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0
Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 0
---
Satisfied in distance/logic within a given contig pair (pre-scaffold): 0
Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 33
---
Total satisfied: 0 unsatisfied: 33


Estimated insert size statistics (based on 0 pairs):
Mean insert size = 0
Median insert size = 0

REPEATS:
Number of repeated edges = 0
------------------------------------------------------------

################################################################################

SUMMARY:
------------------------------------------------------------
Inserted contig file;
Total number of contigs = 1058
Sum (bp) = 35688531
Total number of N's = 0
Sum (bp) no N's = 35688531
GC Content = 45.29%
Max contig size = 382053
Min contig size = 300
Average contig size = 33732
N25 = 162114
N50 = 88961
N75 = 48154

After scaffolding lib1:
Total number of scaffolds = 1058
Sum (bp) = 35688531
Total number of N's = 0
Sum (bp) no N's = 35688531
GC Content = 45.39%
Max scaffold size = 382053
Min scaffold size = 300
Average scaffold size = 33732
N25 = 162114
N50 = 88961
N75 = 48154

------------------------------------------------------------

Can anyone help me to understand why it is coming like this?

Any help will be appreciate..

Thanks in advance....
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