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treangenlab / emu

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Short Read single and paired end Emu Command Line #4

Closed arpit20328 closed 3 months ago

arpit20328 commented 6 months ago

Dear Authors (of Emu):

I am using Emu pipeline on some of Illumina based FASTQ files which are short read. Emu defines that it can run on short read sequences as well by introduction of --type sr command line.

I wanted to know what is the range of short read (base pairs) Emu could act on ?

Is Emu compatible with short read sequencing data of Illumina ? then of what range (base pairs)

Regards Arpit

kdc10 commented 3 months ago

The only test results that have been evaluated by us are the results provided in the manuscript ( https://doi.org/10.1038/s41592-022-01520-4). For short reads with Emu, minimap2 with the type -sr is used for alignment. Therefore, we expect Emu to be compatible with length/region that aligns well with your database with minimap2 short read settings.