.paf file for chimera checking

[a-89]

Dear Heng,

I am using Minimap2 with full-length 16S rRNA ONT reads in a mock community. As seen, in other issues using -c or not changed my .paf results. I am using this -paf file to further remove chimera (with yacrd).

I just wanted to be sure, that -c option gives more accurate results since without -c option they appear much more chimeric reads than when using -c. When splitting these "chimeric" reads and blasting them, they seem chimeric. But maybe is due to the high similarity of the 16S rRNA gene (I attached two sequences as an example: chimera_or_not.txt).

Minimap2 output:
##Without -c option, the read 3984e626-4c77-4461-99d2-dcac7d389900 will be considered chimeric

3984e626-4c77-4461-99d2-dcac7d389900	1407	654	1401	-	Lactobacillus_fermentum_complete_genome	1905333	1889994	1890758	434	767	0	tp:A:P	cm:i:51	s1:i:432	s2:i:432	dv:f:0.0639
3984e626-4c77-4461-99d2-dcac7d389900	1407	654	1401	+	Lactobacillus_fermentum_complete_genome	1905333	1229551	1230315	434	767	0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639
3984e626-4c77-4461-99d2-dcac7d389900	1407	654	1401	-	Lactobacillus_fermentum_complete_genome	1905333	20179	20943	434	767	0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639
3984e626-4c77-4461-99d2-dcac7d389900	1407	654	1401	-	Lactobacillus_fermentum_complete_genome	1905333	411724	412488	434	767	0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639
3984e626-4c77-4461-99d2-dcac7d389900	1407	654	1401	-	Lactobacillus_fermentum_complete_genome	1905333	97074	97838	434	767	0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639
3984e626-4c77-4461-99d2-dcac7d389900	1407	20	466	-	Staphylococcus_aureus_chromosome	2718780	728964	729429	158	466	11	tp:A:P	cm:i:16	s1:i:155	s2:i:141	dv:f:0.0935
3984e626-4c77-4461-99d2-dcac7d389900	1407	20	466	+	Staphylococcus_aureus_chromosome	2718780	2091147	2091612	144	466	0	tp:A:S	cm:i:14	s1:i:141	dv:f:0.1024

##However, with the -c option this read will be considered okay

3984e626-4c77-4461-99d2-dcac7d389900	1407	5	1404	+	Lactobacillus_fermentum_complete_genome	1905333	1228882	1230318	1279	1463	0	NM:i:184	ms:i:1768	AS:i:1768	nn:i:0	tp:A:P	cm:i:51	s1:i:432	s2:i:432	dv:f:0.0639	cg:Z:40M2D5M1I27M2D36M4D15M1D28M1D44M1D4M1D9M1I10M3I3M1D38M1D31M1D3M1I3M1D11M1D13M2D3M2I75M1I2M2D6M2D2M5D14M2I6M1D3M1I34M2D30M1I54M1D4M1D150M1I45M1D62M2I3M1D2M2D42M4D22M1D1M1D59M1I13M2D33M2D9M2D54M1I6M2D14M1D15M1I7M1I57M1D24M1I8M1D13M2D4M1D4M2I15M2D1M1I6M2I40M1D5M3D17M1I55M1D33M
3984e626-4c77-4461-99d2-dcac7d389900	1407	5	1404	-	Lactobacillus_fermentum_complete_genome	1905333	20176	21612	1279	1466	0	NM:i:187	ms:i:1768	AS:i:1768	nn:i:0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639	cg:Z:32M1D55M1I16M3D3M1D43M5I3M2D3M2D11M2I7M1D3M2D14M1D8M1I22M1D57M1I9M1I16M1D14M2D3M1I56M2D10M2D30M2D14M1I60M1D2M1D19M4D44M2D2M3I3M2D62M1D43M1I151M1D5M1D51M1I33M2D33M1I4M1D5M2I14M5D3M2D5M2D3M1I75M2I3M2D12M1D12M1D2M1I3M1D29M1D41M1D3M3I8M1I11M1D2M1D46M1D27M1D15M4D37M2D25M1I3M2D44M
3984e626-4c77-4461-99d2-dcac7d389900	1407	5	1404	-	Lactobacillus_fermentum_complete_genome	1905333	97071	98507	1279	1466	0	NM:i:187	ms:i:1768	AS:i:1768	nn:i:0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639	cg:Z:32M1D55M1I16M3D3M1D43M5I3M2D3M2D11M2I7M1D3M2D14M1D8M1I22M1D57M1I9M1I16M1D14M2D3M1I56M2D10M2D30M2D14M1I60M1D2M1D19M4D44M2D2M3I3M2D62M1D43M1I151M1D5M1D51M1I33M2D33M1I4M1D5M2I14M5D3M2D5M2D3M1I75M2I3M2D12M1D12M1D2M1I3M1D29M1D41M1D3M3I8M1I11M1D2M1D46M1D27M1D15M4D37M2D25M1I3M2D44M
3984e626-4c77-4461-99d2-dcac7d389900	1407	5	1404	-	Lactobacillus_fermentum_complete_genome	1905333	1889991	1891427	1278	1466	0	NM:i:188	ms:i:1762	AS:i:1762	nn:i:0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639	cg:Z:31M1D56M1I16M3D3M1D43M5I3M2D3M2D11M2I7M1D3M2D14M1D8M1I22M1D57M1I9M1I16M1D14M2D3M1I56M2D10M2D30M2D14M1I60M1D2M1D19M4D44M2D2M3I3M2D62M1D43M1I151M1D5M1D51M1I33M2D33M1I4M1D5M2I14M5D3M2D5M2D3M1I75M2I3M2D12M1D12M1D2M1I3M1D29M1D41M1D3M3I8M1I11M1D2M1D46M1D27M1D15M4D37M2D25M1I3M2D44M
3984e626-4c77-4461-99d2-dcac7d389900	1407	5	1404	-	Lactobacillus_fermentum_complete_genome	1905333	411721	413167	1281	1476	0	NM:i:195	ms:i:1752	AS:i:1752	nn:i:0	tp:A:S	cm:i:51	s1:i:432	dv:f:0.0639	cg:Z:32M1D55M1I16M3D3M1D43M5I3M2D3M2D11M2I7M1D3M2D14M1D8M1I22M1D57M1I9M1I16M1D14M2D3M1I56M2D10M2D30M2D14M1I60M1D2M1D19M4D44M2D2M3I3M2D62M1D43M1I151M1D5M1D51M1I33M2D33M1I4M1D5M2I14M5D3M2D5M2D3M1I75M2I3M2D12M1D12M1D2M1I3M1D29M1D41M1D3M3I8M1I11M1D2M1D46M1D27M1D15M4D6M4D3M6D28M2D25M1I3M2D44M

[lh3]

-c is better.

[a-89]

Thanks Heng! Sorry for the duplicated issue!

I was wondering if changing some other parameters would allow identifying more chimeric reads. I am working with 1,500 bp reads that are highly similar (16S rRNA) and I have seen through BLAST more chimeric reads that the ones reported by default settings...

Would it make sense to lower -g parameter? Any other suggestions?

Thanks again!

[lh3]

Reduce -z.