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Gisaid assembly files produced for empty consensus fastas #153

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michellescribner opened this issue Jun 16, 2022 · 0 comments
Open

Gisaid assembly files produced for empty consensus fastas #153

michellescribner opened this issue Jun 16, 2022 · 0 comments

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@michellescribner
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If a sample with very low coverage results in an empty consensus assembly file, the number_N column created by the theiacov workflows will show 0 Ns. The Mercury Prep workflow then produces gisaid assembly files for that sample because they have less Ns than the maximum allowed value. However, the Mercury Batch workflow will exclude the sample from the concatenated assembly.

@michellescribner michellescribner changed the title Empty consensus assembly files result in "number_N = 0" Gisaid assembly files produced for empty consensus fastas Jun 16, 2022
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