Optical map guided genome assembly

Leinonen, Miika; Salmela, Leena

doi:10.1186/s12859-020-03623-1

BMC Bioinformatics

Table 3 Comparison of C. elegans post-coloring contig assembly results with different read coloring schemes. Results are obtained by running Quality Assessment Tool for Genome Assemblies, QUAST 5.0.2, on the contigs and reference genome with ‘–large’ argument

From: Optical map guided genome assembly

C. elegans pre-coloring contig results using miniasm
Minimum	Read	Extended	Adjusted	Number of	Length of	Mis-	NGA50
s-score	coloring	coloring	coloring	contigs	contigs [Kbp]	assemblies	[Kbp]
-	-	-	-	111	100 430	11	2 656
C. elegans post-coloring contig results usingOpticalKermitwith color propagation
Minimum	Read	Extended	Adjusted	Number of	Length of	Mis-	NGA50
s-score	coloring	coloring	coloring	contigs	contigs [Kbp]	assemblies	[Kbp]
0	Only best	No	No	123	97 709	6	2 868
0	Best colored	No	No	162	97 408	6	1 741
0	Best hi-scoring	No	No	150	98 341	8	2 868
0	Only best	Yes	No	123	97 709	6	2 868
0	Best colored	Yes	No	162	97 408	6	1 741
0	Best hi-scoring	Yes	No	151	98 368	8	2 868
15	Only best	No	No	119	97 562	6	2 868
15	Best colored	No	No	157	97 274	6	1 741
15	Best hi-scoring	No	No	151	98 320	8	2 868
15	Only best	Yes	No	119	97 562	6	2 868
15	Best colored	Yes	No	157	97 274	6	1 741
15	Best hi-scoring	Yes	No	152	98 347	10	2 868
0	Only best	No	Yes	119	97 713	7	2 868
0	Best colored	No	Yes	162	97 434	6	1 741
0	Best hi-scoring	No	Yes	148	98 375	8	2 868
0	Only best	Yes	Yes	119	97 713	7	2 868
0	Best colored	Yes	Yes	162	97 434	6	1 741
0	Best hi-scoring	Yes	Yes	152	98 421	8	2 868
15	Only best	No	Yes	115	97 566	7	2 868
15	Best colored	No	Yes	157	97 300	6	1 741
15	Best hi-scoring	No	Yes	149	98 354	10	2 868
15	Only best	Yes	Yes	115	97 566	7	2 868
15	Best colored	Yes	Yes	157	97 300	6	1 741
15	Best hi-scoring	Yes	Yes	153	98 399	10	2 868
C. elegans post-coloring contig results usingOpticalKermitwithout color propagation
Minimum	Read	Extended	Adjusted	Number of	Length of	Mis-	NGA50
s-score	coloring	coloring	coloring	contigs	contigs [Kbp]	assemblies	[Kbp]
0	Only best	No	No	93	100 192	8	2 868
0	Best colored	No	No	92	100 175	11	2 683
0	Best hi-scoring	No	No	131	100 022	10	2 868
0	Only best	Yes	No	93	100 192	8	2 868
0	Best colored	Yes	No	92	100 175	11	2 683
0	Best hi-scoring	Yes	No	130	100 019	10	2 868
15	Only best	No	No	102	100 414	10	2 868
15	Best colored	No	No	96	100 270	12	2 683
15	Best hi-scoring	No	No	131	99 982	12	2 868
15	Only best	Yes	No	102	100 414	10	2 868
15	Best colored	Yes	No	96	100 270	12	2 683
15	Best hi-scoring	Yes	No	130	99 979	12	2 868
0	Only best	No	Yes	94	100 215	8	3 028
0	Best colored	No	Yes	92	100 200	11	2 683
0	Best hi-scoring	No	Yes	133	100 077	10	2 868
0	Only best	Yes	Yes	94	100 215	8	3 028
0	Best colored	Yes	Yes	92	100 200	11	2 683
0	Best hi-scoring	Yes	Yes	133	100 086	10	2 868
15	Only best	No	Yes	103	100 436	10	3 028
15	Best colored	No	Yes	96	100 296	12	2 683
15	Best hi-scoring	No	Yes	133	100 037	12	2 868
15	Only best	Yes	Yes	103	100 436	10	3 028
15	Best colored	Yes	Yes	96	100 296	12	2 683
15	Best hi-scoring	Yes	Yes	133	100 046	12	2 868

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