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Old 12-12-2010, 03:27 AM   #1
katussa10
Member
 
Location: Columbus, OH, USA

Join Date: Jun 2010
Posts: 11
Default Velvet assembly

I have run velvet for hash length 31 and 51 without setting any parameters.Then I calculated exp_cov and cov_cutoff using given perl script (velvet-estimate-exp_cov.pl).

For the hash 31, I found velvetg parameters exp_cov and cov_cutoff to be 1 and 0. I expected these values to go further down for hash 51 (since higher K-mer gives lower coverage). But surprisingly, it was 17 and 0. I have attached the outputs of the perl script for two hash lengths.

Could anyone explain this?

Expected coverage

1 | 19 |
2 | 16 |
3 | 3 |
4 | 36 | *
5 | 66 | **
6 | 69 | **
7 | 108 | ****
8 | 119 | ****
9 | 169 | ******
10 | 196 | ********
11 | 261 | **********
12 | 327 | *************
13 | 503 | ********************
14 | 635 | **************************
15 | 970 | ***************************************
16 | 1210 | *************************************************
17 | 1459 | ************************************************************
18 | 1330 | ******************************************************
19 | 951 | ***************************************
20 | 545 | **********************
21 | 286 | ***********
22 | 160 | ******
23 | 84 | ***
24 | 48 | *
25 | 36 | *
26 | 20 |
27 | 12 |
28 | 10 |
29 | 11 |
30 | 10 |
31 | 8 |
32 | 6 |
33 | 8 |
34 | 3 |
35 | 3 |
36 | 2 |
37 | 2 |
38 | 3 |
39 | 4 |
40 | 1 |
43 | 1 |
44 | 2 |
45 | 1 |
47 | 1 |
48 | 1 |
49 | 2 |
50 | 1 |
51 | 1 |
53 | 1 |
55 | 1 |
61 | 2 |
66 | 1 |
67 | 1 |
74 | 1 |
77 | 2 |
85 | 1 |
86 | 2 |
87 | 1 |
93 | 1 |
95 | 2 |
105 | 2 |
114 | 1 |
127 | 1 |
138 | 1 |
139 | 1 |
142 | 1 |
144 | 1 |
145 | 1 |
147 | 1 |
157 | 1 |
169 | 1 |
173 | 1 |
178 | 1 |
185 | 1 |
219 | 1 |
236 | 1 |
263 | 1 |
273 | 1 |
278 | 1 |
291 | 1 |
312 | 1 |
313 | 1 |
316 | 1 |
317 | 1 |
324 | 1 |
329 | 1 |
332 | 1 |
347 | 1 |
350 | 1 |
366 | 1 |
369 | 1 |
371 | 1 |
399 | 1 |
411 | 1 |
430 | 1 |
433 | 1 |
455 | 1 |
492 | 1 |
502 | 1 |
506 | 1 |
522 | 1 |
546 | 1 |
561 | 1 |
706 | 1 |
775 | 1 |
Predicted expected coverage: 17
velvetg parameters: -exp_cov 17 -cov_cutoff 0

Observed results

1 | 2773 | ************************************************************
2 | 1740 | *************************************
3 | 374 | ********
4 | 41 |
5 | 14 |
6 | 5 |
7 | 4 |
8 | 3 |
9 | 8 |
10 | 12 |
11 | 17 |
12 | 19 |
13 | 28 |
14 | 30 |
15 | 54 | *
16 | 63 | *
17 | 83 | *
18 | 110 | **
19 | 154 | ***
20 | 174 | ***
21 | 233 | *****
22 | 260 | *****
23 | 339 | *******
24 | 400 | ********
25 | 493 | **********
26 | 595 | ************
27 | 681 | **************
28 | 835 | ******************
29 | 897 | *******************
30 | 1148 | ************************
31 | 1234 | **************************
32 | 1449 | *******************************
33 | 1500 | ********************************
34 | 1661 | ***********************************
35 | 1839 | ***************************************
36 | 1972 | ******************************************
37 | 2150 | **********************************************
38 | 2208 | ***********************************************
39 | 2235 | ************************************************
40 | 2469 | *****************************************************
41 | 2433 | ****************************************************
42 | 2528 | ******************************************************
43 | 2467 | *****************************************************
44 | 2462 | *****************************************************
45 | 2387 | ***************************************************
46 | 2403 | ***************************************************
47 | 2281 | *************************************************
48 | 2206 | ***********************************************
49 | 2101 | *********************************************
50 | 1981 | ******************************************
51 | 1866 | ****************************************
52 | 1661 | ***********************************
53 | 1640 | ***********************************
54 | 1558 | *********************************
55 | 1402 | ******************************
56 | 1328 | ****************************
57 | 1154 | ************************
58 | 1093 | ***********************
59 | 1016 | *********************
60 | 907 | *******************
61 | 842 | ******************
62 | 789 | *****************
63 | 730 | ***************
64 | 603 | *************
65 | 631 | *************
66 | 527 | ***********
67 | 499 | **********
68 | 437 | *********
69 | 353 | *******
70 | 333 | *******
71 | 356 | *******
72 | 280 | ******
73 | 261 | *****
74 | 249 | *****
75 | 255 | *****
76 | 215 | ****
77 | 172 | ***
78 | 164 | ***
79 | 137 | **
80 | 143 | ***
81 | 132 | **
82 | 119 | **
83 | 118 | **
84 | 79 | *
85 | 74 | *
86 | 67 | *
87 | 84 | *
88 | 67 | *
89 | 64 | *
90 | 46 |
91 | 59 | *
92 | 44 |
93 | 47 | *
94 | 43 |
95 | 24 |
96 | 29 |
97 | 25 |
98 | 26 |
99 | 20 |
100 | 20 |
101 | 12 |
102 | 16 |
103 | 12 |
104 | 11 |
105 | 11 |
106 | 13 |
107 | 12 |
108 | 7 |
109 | 6 |
110 | 6 |
111 | 4 |
112 | 7 |
113 | 10 |
114 | 6 |
115 | 2 |
116 | 3 |
117 | 2 |
119 | 1 |
120 | 5 |
121 | 3 |
122 | 2 |
123 | 4 |
125 | 3 |
126 | 3 |
127 | 2 |
128 | 1 |
129 | 1 |
130 | 1 |
134 | 2 |
135 | 1 |
136 | 3 |
137 | 2 |
141 | 3 |
142 | 1 |
146 | 3 |
147 | 1 |
148 | 1 |
150 | 2 |
151 | 3 |
153 | 1 |
158 | 1 |
166 | 1 |
170 | 1 |
175 | 1 |
179 | 1 |
181 | 1 |
185 | 1 |
186 | 1 |
190 | 1 |
196 | 2 |
201 | 1 |
206 | 2 |
207 | 1 |
209 | 1 |
217 | 1 |
221 | 1 |
222 | 1 |
227 | 1 |
229 | 1 |
237 | 1 |
241 | 1 |
243 | 1 |
258 | 1 |
261 | 1 |
262 | 1 |
267 | 1 |
269 | 1 |
272 | 1 |
273 | 1 |
282 | 1 |
287 | 1 |
288 | 1 |
290 | 1 |
294 | 1 |
295 | 1 |
299 | 1 |
303 | 1 |
310 | 1 |
318 | 1 |
321 | 1 |
324 | 1 |
325 | 1 |
329 | 1 |
330 | 2 |
332 | 1 |
334 | 1 |
340 | 1 |
341 | 2 |
347 | 1 |
359 | 1 |
360 | 1 |
361 | 1 |
363 | 1 |
368 | 1 |
373 | 1 |
376 | 1 |
380 | 1 |
404 | 1 |
411 | 1 |
422 | 1 |
434 | 1 |
435 | 1 |
444 | 1 |
451 | 2 |
463 | 1 |
464 | 1 |
465 | 1 |
473 | 1 |
500 | 1 |
510 | 1 |
514 | 1 |
516 | 1 |
524 | 1 |
551 | 1 |
558 | 1 |
561 | 1 |
562 | 1 |
589 | 1 |
610 | 1 |
637 | 1 |
645 | 1 |
674 | 1 |
716 | 1 |
718 | 1 |
741 | 1 |
775 | 1 |
777 | 1 |
778 | 1 |
787 | 1 |
797 | 1 |
806 | 1 |
826 | 1 |
861 | 1 |
862 | 1 |
880 | 1 |
937 | 1 |
949 | 1 |
962 | 1 |
965 | 1 |
971 | 1 |
979 | 1 |
983 | 1 |
1003 | 1 |
1036 | 1 |
1064 | 1 |
1087 | 1 |
1100 | 1 |
1287 | 1 |
1342 | 1 |
1365 | 1 |
1408 | 1 |
1433 | 1 |
1512 | 1 |
1649 | 1 |
Predicted expected coverage: 1
velvetg parameters: -exp_cov 1 -cov_cutoff 0
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Old 12-12-2010, 06:26 AM   #2
jts
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Location: Cambridge

Join Date: Feb 2009
Posts: 22
Default

It looks like the perl script simply selects the mode of the k-mer frequency histogram: 1 and 17 are the most frequent values in the two histograms you show. The histogram for k=31 looks as expected to me (many low-frequency k-mers which represent k-mers with sequencing errors then a proper distribution of k-mers around 40-45X). The k=51 histogram does not look right. I would guess the k=51 assembly failed for some reason - probably not enough coverage to support that high kmer length.

I suggest trying the VelvetOptimiser script which is included with velvet.

Last edited by jts; 12-12-2010 at 08:03 AM.
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Old 12-12-2010, 10:22 AM   #3
katussa10
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Location: Columbus, OH, USA

Join Date: Jun 2010
Posts: 11
Default

Thanks a lot jts. I will try velvetOptimiser.
katussa10 is offline   Reply With Quote
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