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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
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Insertion detected when using mafft and not when using racon #55

Open waltergallegog opened 9 months ago

waltergallegog commented 9 months ago

Hello, I was wondering if it is expected for an insertion to be detected when using mafft and not detected when using racon. My understanding is that the use of racon would improve the identification of the breakpoint position and length of the insertion. Is it expected to also affect the insertions detected?

Attached the output of nanomonsv in debug mode, resulting from running it the region chr1:1-2000000, where the insertion is detected when using mafft, and a screenshot of IGV in the position.

I more details can be of help please let me know.

Detected insertion:

chr1    1099878 i_0 C   <INS>   .   PASS    END=1099878;SVTYPE=INS;SVINSLEN=961;SVINSSEQ=TCCACTATTAT...     TR:VR   66:9    43:0

sample11_chr1_1-2000000_mafft.tar.gz

sample11_chr1_1-2000000_racon.tar.gz

image

zhemingfan commented 9 months ago

Just noting that I'm encountering the same kind of results.