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Are there minimum requirements from a de novo genome assembly for it to be suitably used as a reference for SNP calling?

To what extent does a de novo genome need to be assembled for it to be used as a reference? If I have a de novo assembly for a large mammalian genome comprising of a under 1M contigs (Illumina + PacBio), and I want to call SNPs against this reference from samples that have been sequenced (shallow 5x-10x Illumina short read data), will it work well?

What would be the parameters to tweak for alignment, variant calling, and what would be the warning signs to look out for? Thank you

snp assembly reference genome snp wgs
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written by nancy nancy

comprising of a under 1M contigs

1,000,000 (one million) contigs? Or 1,000 (one thousand) contigs?

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written by h.mon h.mon

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