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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Selecting a seed #133

Closed dcraheem closed 4 years ago

dcraheem commented 4 years ago

The mt genomes I am assembling using novoplasty represent several species in a single land-snail genus. I have previously assembled and annotated complete mt genomes for other species in this same genus.

1) Would the sequence of a highly-conserved gene (e.g. cox1, cox2 or cox3) from one of these previously assembled genomes make a suitable seed for my novoplasty assembly?

2) If I use a gene like cox1, should the sequence of the whole gene be used? For my genus, the total length of the cox 1 gene is c. 1600 bp (700-800 bp for the cox 2 and cox 3 genes).

ndierckx commented 4 years ago

seed doesn't matter, can use a mouse sequence for human, still works length doesn't matter as long not shorter than the read length, probably will only use the first 100 to 200 bp anyway

dcraheem commented 4 years ago

Do you mean that novoplasty probably uses only the first 100-200bp of the seed sequence?

ndierckx commented 4 years ago

Yes, unless it doesn't finds a match there, it will continue further

dcraheem commented 4 years ago

Thanks very much for the advice and the software.