chm13_asm_ctgs_2021_0104 / Jason Chin

Genome assembly of the CHM13 cell line. Done with a new assembler based on the SHIMMER indexing method. The run time is 1.6 hours with 64 core aarch CPUs. The wall clock time is about 1.6 hours. 

2021-01-04 08:47:07,980 INFO  [pg_asm::utils::layout] Total size: 3055717214
2021-01-04 08:47:07,980 INFO  [pg_asm::utils::layout] Longest size: 140284871
2021-01-04 08:47:07,980 INFO  [pg_asm::utils::layout] N50: 82577644
2021-01-04 08:47:07,980 INFO  [pg_asm::utils::layout] N90: 17313701
2021-01-04 08:47:07,980 INFO  [pg_asm::utils::layout] Number of contigs: 357
2021-01-04 08:47:07,980 INFO  [pg_asm::utils::layout] Number of Contigs > 100kb: 207

2021-01-04 08:48:22,512 INFO  [pg_asm] pg_asm run end
2021-01-04 08:48:22,512 INFO  [pg_asm] total user cpu time: 272568 seconds = 75.71333 hours
2021-01-04 08:48:22,512 INFO  [pg_asm] total system cpu time: 920 seconds = 0.25555554 hours
2021-01-04 08:48:22,512 INFO  [pg_asm] total elapse time: 5773.4155 seconds = 1.6037266 hours

Here is the result of the CHM13 BAC coverage with the assembly

Checking attempted with maximum distance from contig end of 1000 bp..Done
******************* BAC SUMMARY ******************
 TOTAL    : 341
 BP       : 51532183
************** Statistics for: _test9.fa ****************
BACs closed: 330 (96.7742); BACs attempted: 341 %good = 96.7742; BASES 49874385 (96.783)
Median:          99.99135
MedianQV:        40.62984
Mean:            99.94396
MeanQV:          32.51511
***** STATS IGNORING INDELS ********************
Median:          100
MedianQV:        Inf
Mean:            99.99418
MeanQV:          42.34828
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