statistics of assembly results

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

GNU General Public License v3.0

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statistics of assembly results #154

Closed yangxiaofeill closed 5 years ago

yangxiaofeill commented 5 years ago

Hi Dr. Ruan, I have tried your assembler wtdbg2, and get the raw.fa file. However, I cannot find the statistic results of the assembly. Could you tell me how to get it?

Best

ruanjue commented 5 years ago

Run https://github.com/ruanjue/wtdbg2/blob/master/scripts/seq_n50.pl on the raw.fa

yangxiaofeill commented 5 years ago

Thanks

cement-head commented 4 years ago

Not quite sure how to interpret the output of your script - why are there TWO numbers associated with each N## score?

$ ./seq_n50.pl input.fa Total: 6200959339 Count: 82732 Average: 74952.37 Median: 22459 N00: 5280931 1 N10: 1469795 309 N20: 1026989 823 N30: 737002 1540 N40: 535766 2528 N50: 369759 3921 N60: 224078 6063 N70: 101664 10211 N80: 51089 19151 N90: 26812 35933 N100: 1387 82732

ruanjue commented 4 years ago

The first num is N50, the second is L50.