Sean’s Notebook: Oly Genome re-assembly, try 2.

Finished the Redundans run on the Oly genome with a smaller k-mer length, and things look much better!

Full Scaffold stats:

D-173-250-161-130:NewOlyAssembly Sean$ assembly-stats scaffolds.fa
stats for scaffolds.fa
sum = 567422454, n = 337054, ave = 1683.48, largest = 74226
N50 = 3492, n = 44086
N60 = 2683, n = 62641
N70 = 1989, n = 87196
N80 = 1355, n = 121603
N90 = 737, n = 177120
N100 = 200, n = 337054
N_count = 30184511
Gaps = 286008

Reduced Scaffold stats:

D-173-250-161-130:NewOlyAssembly Sean$ assembly-stats scaffolds.reduced.fa
stats for scaffolds.reduced.fa
sum = 546928670, n = 300593, ave = 1819.50, largest = 78788
N50 = 3852, n = 36149
N60 = 2917, n = 52500
N70 = 2137, n = 74420
N80 = 1455, n = 105359
N90 = 810, n = 155023
N100 = 200, n = 300593
N_count = 5238187
Gaps = 209203

Full Contig stats:

D-173-250-161-130:NewOlyAssembly Sean$ assembly-stats contigs.fa
stats for contigs.fa
sum = 1633553496, n = 12395459, ave = 131.79, largest = 23341
N50 = 141, n = 2124062
N60 = 115, n = 3463771
N70 = 92, n = 5003872
N80 = 69, n = 7087338
N90 = 61, n = 9624083
N100 = 58, n = 12395459
N_count = 0
Gaps = 0

Reduced Contig stats:

D-173-250-161-130:NewOlyAssembly Sean$ assembly-stats contigs.reduced.fa
stats for contigs.reduced.fa
sum = 532736649, n = 791403, ave = 673.15, largest = 23341
N50 = 940, n = 151868
N60 = 726, n = 216469
N70 = 553, n = 300627
N80 = 408, n = 412850
N90 = 289, n = 568264
N100 = 200, n = 791403
N_count = 0
Gaps = 0

Complete Contig fasta: here

Reduced Contig fasta: here

Complete scaffold fasta: here

Reduced scaffold fasta: here

SLURM execution script: here

Redundans output: here

All data: here

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