Hi,
I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew the approximate chloroplast genome size (165kb) and the mitochondrial genome is ~1 MB. But I do not know the depth coverage and expected genome size. I am very beginner and don't know how to calculate both depth coverage and genome size. I have used jellyfish and 27 kmer length to calculate the genome size but not able to get a good result.
input parameter:
./jellyfish count -m 27 -s 100M -t 10 -C ONT.fastq
Please help me to find out the expected genome size.
Thank you.
0 0
1 7989688383
2 166231294
3 43211315
4 18926377
5 10427587
6 6516393
7 4405895
8 3149285
9 2350173
10 1813597
11 1432766
12 1158622
13 951965
14 795509
15 672888
16 575600
17 498467
18 434147
19 381189
20 336466
21 300410
22 266885
23 240702
24 217316
25 196646
26 179063
27 163313
28 149618
29 137855
30 127116
31 118281
32 109350
33 101433
34 93983
35 88034
36 82194
37 76527
38 72389
39 67914
40 63928
41 60617
42 56686
43 53516
44 50601
45 48133
46 45279
47 43027
48 40740
49 39054
50 37361
51 35388
52 33732
53 32167
54 30755
55 29465
56 28173
57 27398
58 26459
59 25056
60 23864
61 22928
62 22162
63 21486
64 20181
65 19742
66 19118
67 18670
68 17906
69 17303
70 16777
71 16305
72 15511
73 15204
74 14489
75 13917
76 13576
77 13311
78 12835
79 12391
80 12081
81 11619
82 11245
83 11060
84 10732
85 10415
86 10206
87 9634
88 9545
89 9411
90 9189
91 8677
92 8589
93 8439
94 8109
95 7837
96 7888
97 7397
98 7410
99 7198
100 7050
101 6807
102 6619
103 6529
104 6439
105 6244
106 6109
107 6142
108 5897
109 5642
110 5619
111 5466
112 5309
113 5252
114 5170
115 4965
116 4892
117 4785
118 4604
119 4561
120 4545
121 4418
122 4498
123 4306
124 4235
125 4072
126 3929
127 3961
128 3912
129 3702
130 3737
131 3631
132 3505
133 3537
134 3440
135 3346
136 3321
137 3261
138 3247
139 3063
140 3174
141 3070
142 3152
143 2913
144 2933
145 2868
146 2733
147 2736
148 2683
149 2722
150 2576
151 2558
152 2647
153 2599
154 2397
155 2474
156 2405
157 2349
158 2358
159 2302
160 2283
161 2203
162 2246
163 2204
164 2178
165 2134
166 2097
167 2127
168 2074
169 2066
170 1989
171 2029
172 1917
173 1965
174 1946
175 1843
176 1903
177 1877
178 1928
179 1873
180 1840
181 1864
182 1778
183 1812
184 1741
185 1719
186 1740
187 1750
188 1684
189 1712
190 1717
191 1647
192 1608
193 1630
194 1609
195 1633
196 1621
197 1598
198 1526
199 1583
200 1564
I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew the approximate chloroplast genome size (165kb) and the mitochondrial genome is ~1 MB. But I do not know the depth coverage and expected genome size. I am very beginner and don't know how to calculate both depth coverage and genome size. I have used jellyfish and 27 kmer length to calculate the genome size but not able to get a good result.
input parameter:
./jellyfish count -m 27 -s 100M -t 10 -C ONT.fastq
Please help me to find out the expected genome size.
Thank you.
0 0
1 7989688383
2 166231294
3 43211315
4 18926377
5 10427587
6 6516393
7 4405895
8 3149285
9 2350173
10 1813597
11 1432766
12 1158622
13 951965
14 795509
15 672888
16 575600
17 498467
18 434147
19 381189
20 336466
21 300410
22 266885
23 240702
24 217316
25 196646
26 179063
27 163313
28 149618
29 137855
30 127116
31 118281
32 109350
33 101433
34 93983
35 88034
36 82194
37 76527
38 72389
39 67914
40 63928
41 60617
42 56686
43 53516
44 50601
45 48133
46 45279
47 43027
48 40740
49 39054
50 37361
51 35388
52 33732
53 32167
54 30755
55 29465
56 28173
57 27398
58 26459
59 25056
60 23864
61 22928
62 22162
63 21486
64 20181
65 19742
66 19118
67 18670
68 17906
69 17303
70 16777
71 16305
72 15511
73 15204
74 14489
75 13917
76 13576
77 13311
78 12835
79 12391
80 12081
81 11619
82 11245
83 11060
84 10732
85 10415
86 10206
87 9634
88 9545
89 9411
90 9189
91 8677
92 8589
93 8439
94 8109
95 7837
96 7888
97 7397
98 7410
99 7198
100 7050
101 6807
102 6619
103 6529
104 6439
105 6244
106 6109
107 6142
108 5897
109 5642
110 5619
111 5466
112 5309
113 5252
114 5170
115 4965
116 4892
117 4785
118 4604
119 4561
120 4545
121 4418
122 4498
123 4306
124 4235
125 4072
126 3929
127 3961
128 3912
129 3702
130 3737
131 3631
132 3505
133 3537
134 3440
135 3346
136 3321
137 3261
138 3247
139 3063
140 3174
141 3070
142 3152
143 2913
144 2933
145 2868
146 2733
147 2736
148 2683
149 2722
150 2576
151 2558
152 2647
153 2599
154 2397
155 2474
156 2405
157 2349
158 2358
159 2302
160 2283
161 2203
162 2246
163 2204
164 2178
165 2134
166 2097
167 2127
168 2074
169 2066
170 1989
171 2029
172 1917
173 1965
174 1946
175 1843
176 1903
177 1877
178 1928
179 1873
180 1840
181 1864
182 1778
183 1812
184 1741
185 1719
186 1740
187 1750
188 1684
189 1712
190 1717
191 1647
192 1608
193 1630
194 1609
195 1633
196 1621
197 1598
198 1526
199 1583
200 1564
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