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
Roberts Lab 