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YingZhou001 / Immuannot

Immuological gene typing and annotation for genome assembly
MIT License
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Missed gene detection when there are many samples/contigs #7

Closed ryought closed 4 months ago

ryought commented 4 months ago

Thank you for making such a useful tool. I noticed that some genes are missed when the number of samples (contigs) is large (e.g. 200 or more). I think it may be necessary to set the upper limit of the number of secondary alignments to at least the number of samples with the minimap2 option -N.

YingZhou001 commented 4 months ago

Thanks for reporting this to me! Yes, the current version only supports one sample assembly for each run. I haven't tested different -N values yet. I may consider to include those options in the next version. By the way, may I know what is your case in applying Immuannot? If you have multiple full length genomes, the best practice I suppose is to separate them into each fa or fq file; but if you are looking at the MHC/KIR region, it should be very fast to extract each contig with seqtk.

ryought commented 4 months ago

Okay, thanks for your answer! I want to compare the diversity of the gene regions between HPRC samples and my own samples. I will run the script for each sample individually.