scottgeib
commented
3 years ago It is heterochromatic region, probably centromere, too repetitive for hic reads to map uniquely, but that’s ok because hifi reads assembled right through it. If you want to confirm correctness of this region can map hifi reads and look at depth and see if it matches rest of genome Scott
Scott Geib Research Entomologist USDA ARS Pacific Basin Agricultural Research Center 64 Nowelo St, Hilo, Hawaii 96720
From: jinxin112233 @.> Sent: Tuesday, May 25, 2021 4:38:44 PM To: chhylp123/hifiasm @.> Cc: Subscribed @.***> Subject: [chhylp123/hifiasm] The sequence assembled by hifi is not covered by hic reads (#126)
Hi We assembled a genome with hifiasm and divided the chromosomes with hic reads. However, we found that some contigs are not covered by hic reads. More complicated is that in the figure, the front end of contig is not covered by hic reads, and the back end of congtig is covered by hic reads. We would like to ask what caused this situation? How to improve the assembly？ [图片1]https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F72123585%2F119594458-68ae3900-be0e-11eb-9e9f-ac260f024547.png&data=04%7C01%7C%7Cc5daf0c18d514b299ed008d91fef61d7%7Ced5b36e701ee4ebc867ee03cfa0d4697%7C0%7C0%7C637575935268539285%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ekKUkmudcdsizMzg3mewzleDY1Si%2B53EbVLwfINndlM%3D&reserved=0
Best jx
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jinxin112233
Hi We assembled a genome with hifiasm (typical commands in hic mode) and divided the chromosomes with hic reads. However, we found that some contigs are not covered by hic reads. More complicated is that in the figure, the front end of contig is not covered by hic reads, and the back end of congtig is covered by hic reads. We would like to ask what caused this situation? How to improve the assembly？
Best jx