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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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chloroplast genome totally lost #24

Closed njaupan closed 5 years ago

njaupan commented 5 years ago

Dear Ruanjue, I have used defult paramater for assembling a plant genome, the mitochondrial genome (~400kb) is assembled partly but the chloroplast genome (150kb) is totally lost, do you have any suggestion like adjust some paramater? Best, panpan

ruanjue commented 5 years ago

It depends on the sequencing depth of MT and CP genomes.

Usually, they are too high, and be fitlered as highly repetitive. To avoid this, set wtdmo -K 0, but will be slower.

Otherwise, the depth is too low, please map raw reads to a relative CP genome, and assembly the mapped reads indepenently.

Jue

njaupan commented 5 years ago

Thank you, i will let you know when it's been done.