Minimap2: .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.