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<br> 2021-01-04 08:47:07,980 INFO [pg_asm::utils::layout] Longest size: 140284871<br> 2021-01-04 08:47:07,980 INFO [pg_asm::utils::layout] N50: 82577644<br> 2021-01-04 08:47:07,980 INFO [pg_asm::utils::layout] N90: 17313701<br> 2021-01-04 08:47:07,980 INFO [pg_asm::utils::layout] Number of contigs: 357<br> 2021-01-04 08:47:07,980 INFO [pg_asm::utils::layout] Number of Contigs &gt; 100kb: 207 2021-01-04 08:48:22,512 INFO [pg_asm] pg_asm run end<br> 2021-01-04 08:48:22,512 INFO [pg_asm] total user cpu time: 272568 seconds = 75.71333 hours<br> 2021-01-04 08:48:22,512 INFO [pg_asm] total system cpu time: 920 seconds = 0.25555554 hours<br> 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 <br> Checking attempted with maximum distance from contig end of 1000 bp..Done<br> ******************* BAC SUMMARY ******************<br> TOTAL : 341<br> BP : 51532183<br> ************** Statistics for: _test9.fa ****************<br> BACs closed: 330 (96.7742); BACs attempted: 341 %good = 96.7742; BASES 49874385 (96.783)<br> Median: 99.99135<br> MedianQV: 40.62984<br> Mean: 99.94396<br> MeanQV: 32.51511<br> ***** STATS IGNORING INDELS ********************<br> Median: 100<br> MedianQV: Inf<br> Mean: 99.99418<br> MeanQV: 42.34828<br> **********************************************