Tool for removing Spurious alignments from metagenomic alignment

Question

[vishalchanda364]

Hello, Can anyone suggest the best tool for removing the spurious alignments from my metagenomic aligned data.?

[Fatima]

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If possible please provide more information about what tool you used to do the alignment, what thresholds, ...

Tools for masking low complexity regions

http://meme-suite.org/doc/dust.html

https://drive5.com/usearch/manual/masking.html

http://cbrc3.cbrc.jp/~martin/tantan/