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Hi all,
I'm using SSPACE v2.0 on a set of contigs assembled through Velvet, with parameters
-x = 0
-z = 0
-k = 5
-a = 0.7
-n = 15
-p = 0
Reads library is a 400bp insert PE illumina 2x90bp.
But when connecting overlapping contigs, the soft scaffolds them with a 'N' spacing instead of merging them. Such an issue should have been corrected in the current version of SSPACE ( see http://seqanswers.com/forums/showpos...3&postcount=97 ), but it does not work for me. Moreover, some overlaps are below 50 bp, i.e. the before-correction threshold.
Perhaps it may help, but all cases I checked for show multiple link possibilities.
Did it happened to anyone else with SSPACE v2.0 ?
thanks,
seb.
I'm using SSPACE v2.0 on a set of contigs assembled through Velvet, with parameters
-x = 0
-z = 0
-k = 5
-a = 0.7
-n = 15
-p = 0
Reads library is a 400bp insert PE illumina 2x90bp.
But when connecting overlapping contigs, the soft scaffolds them with a 'N' spacing instead of merging them. Such an issue should have been corrected in the current version of SSPACE ( see http://seqanswers.com/forums/showpos...3&postcount=97 ), but it does not work for me. Moreover, some overlaps are below 50 bp, i.e. the before-correction threshold.
Perhaps it may help, but all cases I checked for show multiple link possibilities.
Did it happened to anyone else with SSPACE v2.0 ?
thanks,
seb.