Sebastien: The LibraryStats indicates AverageOuterDistance of 185, SD 38, number of sequences 72753702
I'm running now with different kmers. Our original run with Ray 2.0.0-rc8 on (I
think) 30 cores took 3 days 5h on a Dell server. I upgraded the Ram on my
little cluster (using 49 cores) so it will run Ray and it's now taking 11-13
hrs with Ray-2.1.0 :). Big change!
There is quite a difference in largest contig. I'm wondering whether it is
legitimate to merge assemblies like some other groups do when assembling with
velvet or Soap?
Ray 2.1.0
Original kmer 21 Ray rc.2.0.8 Cray kmer 21
kmer 31 kmer 45
Contigs >= 100 nt
Number 3500538 2817095 5974696
7161038
Total length 624475006 510215305
945838381 1026747597
Average 178 181
158 143
N50 168
166 146 129
Median 125 122
116 110
Largest 44799 66893
102879 80250
Contigs >= 500 nt
Number 113898 101609
110394 74935
Total length 120187394 116199542
117723390 75591030
Average 1055 1143
1066 1008
N50 1102
1247 1109 1006
Median 738 776
723 692
Largest 44799 66893
102879 80250
Scaffolds >= 100 nt
Number 3496328 2813404
5970969 7158055
Total length 624949147 510625699
946272789 1027132935
Average 178 181
158 143
N50 169
166 146 129
Median 125 122
116 110
Largest 49246 86011
102879 98547
Scaffolds >= 500 nt
Number 111320 99299
108265 73363
Total length 121336504 117181056
118823565 76572975
Average 1089 1180
1097 1043
N50 1160
1313 1164 1065
Median 743 782
727 696
Largest 49246 86011
102879 98547
-----Original Message-----
From: Sébastien Boisvert [mailto:sebastien.boisver...@ulaval.ca]
Sent: December-05-12 11:16 AM
To: Forster, Robert
Cc: denovoassembler-users@lists.sourceforge.net; Jacques Corbeil
Subject: Re: Ray meta?
What do you see in LibraryStatistics.txt ?
This file contains auto-calibrated insert size by Ray.
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