All sequences are low abundance of 20X BGI T7 resequence reads #224
Description
Dear linzhi
I want to assembly mitogenomes of a butterfly from different regions by Mitoz 3.6 in a conda env. But most of the samples failed, some were incomplete assembly, some were stopped with "All sequences are low abundance". My paired reads are 5G respectively, which is resequencing reads of samples from different geographic populations. I calculated that the sequencing depth is 20X, and the Q20 and Q30 of reads are both greater than 90%. I tried a different kmer: 17,19,29,39,49,59,79,99,119,141, also tried different data_size_for_mt_assembly :0, 3, 5, 8, 8, 10, but all failed. I set --min_abundance 9 also only yielded 1kb, I wonder why? Is BGI data unsuitable for assembling mitochondria? Or there's some other reason?
Best regards!