summarystats.md

summary stats of the genome assembly trials done and evaluated for the BOLERO project. verkko assembly evaluation. both the indiviual reports and the summary table is present below for both the evaluation.

completeness based on compleasm ( Total BUSCO searched 425)

ERR10930361ASM	ERR10930362ASM	ERR10930361ASM	ERR10930361ASM
14.12%, 60	6.12%, 26	13.18%, 56	12.71%, 54
85.88%, 365	93.65%, 398	86.82%, 369	87.29%, 371
0.00%, 0	0.24%, 1	0.00%, 0	0.00%, 0
0.00%, 0	0.00%, 0	0.00%, 0	0.00%, 0
0.00%, 0	0.00%, 0	0.00%, 0	0.00%, 0
425	425	425	425

completeness based on BUSCO ( Total BUSCO searched 425)

Species	Complete BUSCO	Complete and single-copy BUSCO	Complete and duplicated BUSCOs (D)	Fragmented BUSCOs (F)	Missing BUSCOs (M)	Completion score
ERR10930361ASM	422	359	63	1	2	99.3%
ERR10930362ASM	421	390	31	3	1	99.1 %
ERR10930361ASM	423	361	62	1	1	99.5 %
ERR10930361ASM	423	367	56	1	1	99.6%

reference genome protein comparison

ERR10930361ASM	ERR10930362ASM	ERR10930361ASM	ERR10930361ASM
65.88%, 280	65.88%, 280	65.88%, 280	65.88%, 280
33.88%, 144	33.88%, 144	33.88%, 144	33.88%, 144
0.00%, 0	0.00%, 0	0.00%, 0	0.00%, 0
0.24%, 1	0.24%, 1	0.24%, 1	0.24%, 1

genome assembly purging before an after using the hifiasm

number of contigs	ERR10930361.asm	ERR10930362.asm	ERR10930363.asm	ERR10930364.asm	ERR10930364_l3.asm
	1248	2593	2611	1640	312

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verkko without purging

ERR10930361.asm	ERR10930362.asm	ERR10930363.asm	ERR10930364.asm
6817	3458	7061	11032

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completeness based on BUSCO for the trio binning method ( Total BUSCO searched 425)

Species	Complete BUSCO	Complete and single-copy BUSCO	Complete and duplicated BUSCOs (D)	Fragmented BUSCOs (F)	Missing BUSCOs (M)	Completion score
hap1	422	415	7	1	2	99.2%
hap2	420	407	13	4	1	98.9%