Entering edit mode
2.7 years ago
K.Gee
▴
40
Hello everyone, I am trying to find the average coverage from a genome. I used Spades for assembling the raw reads with k-mers sizes of 21, 55, 77, 99, and 127
Reading Spades's manual, I found that the average coverage is calculated in a file called Spades.log. I used the command below,
grep -A1 average spades.log
and I got the following results:
0:01:04.922 64M / 9G INFO General (simplification.cpp : 470) Counting average coverage
0:01:04.924 64M / 9G INFO General (simplification.cpp : 476) Average coverage = 270.591
--
0:00:25.204 64M / 9G INFO General (simplification.cpp : 470) Counting average coverage
0:00:25.206 64M / 9G INFO General (simplification.cpp : 476) Average coverage = 264.149
--
0:00:24.370 136M / 9G INFO General (simplification.cpp : 470) Counting average coverage
0:00:24.372 136M / 9G INFO General (simplification.cpp : 476) Average coverage = 253.698
--
0:00:22.537 144M / 9G INFO General (simplification.cpp : 470) Counting average coverage
0:00:22.538 144M / 9G INFO General (simplification.cpp : 476) Average coverage = 242.892
--
0:00:22.398 140M / 9G INFO General (simplification.cpp : 470) Counting average coverage
0:00:22.400 140M / 9G INFO General (simplification.cpp : 476) Average coverage = 226.695
--
0:00:25.091 120M / 9G INFO General (simplification.cpp : 470) Counting average coverage
0:00:25.092 120M / 9G INFO General (simplification.cpp : 476) Average coverage = 195.146
Can anybody explain to me what is the number next to M/9G ? Also, what is the average coverage from the above 5 values that should I consider as “correct” ?
Thank you in advance.
120M / 9G - RAM usage
Thanks for the answer. Is it possible to explain to me briefly the principle of selecting this option
for the average coverage over the others?
It's just for example. All second column is RAM usage.
οκ I see!!!