All sequences are low abundance of 20X BGI T7 resequence reads

[XuanZhang-Black]

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!

[linzhi2013]

Hi XuanZhang,

Did you notice this:

What tissues were used for the resequencing? Some tissues may have a low ratio of MT-reads.

I tested a lot of mammal samples sequenced by BGI, most of their mitogenome were circular. So I don't think sequencing platform is a problem here.

If you do not mind, you can also send me the data of one of your samples to my email: linzhi2012[MitoZ]gmail[MitoZ]com.

Regards

[XuanZhang-Black]

Hi linzhi,

The whole body was used for resequencing. In fact, only 5X illumina reads was useful in my previous study for the same species. And the same problem was occurred in my colleague that also research on insects. This is my resequencing raeds
通过网盘分享的文件：SXCA2_IUDI277_raw_1.fq.gz等2个文件
链接: https://pan.baidu.com/s/1SMoUFGCYflsGixJSE5iloQ?pwd=kqwt 提取码: kqwt
--来自百度网盘超级会员v1的分享

Best regards.

[linzhi2013]

Hi Zhang Xuan,

I have deleted your comment since it is public to all people.

I am currently downloading your data, which may take 30 hours.

Best

[XuanZhang-Black]

Hi, Dr. linzhi,
Is there any progress?