Removes 'low-quality alignments' - what does this mean? - Githubissues

schneebergerlab / syri

Synteny and Rearrangement Identifier

https://schneebergerlab.github.io/syri/

MIT License

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Removes 'low-quality alignments' - what does this mean? #240

Closed c-hazel-f closed 3 months ago

c-hazel-f commented 3 months ago

Hello, I was just wondering what parameters count as 'low quality alignments' for SyRi, if you are able to provide or point me in the direction for more information?

mnshgl0110 commented 3 months ago

Sorry, for a delayed response. Syri selects alignments which are longer than 100bp and have alignment identity >90%. This is reported in the syri.log file as well with the message: Filtering low-quality alignments (alignment quality < 90, alignment length < 100)

Currently, these thresholds are hard-coded: https://github.com/schneebergerlab/syri/blob/cc575be17c69b8ff10e768327f1826a8b837acfa/syri/pyxFiles/synsearchFunctions.pyx#L388

but users are encouraged to adjust them as per their requirements.