Open andreaschavez opened 1 year ago
Hi Andreas,
You are right. You can use a table of contig or scaffold lengths as the input file of "chromosome sizes" or "GENOME_SIZE" for HiC-Pro, and make sure that the lengths exactly match the contig or scaffold sequences. HiC-Pro can handle any genomic sequences, both chromosome-level reference genome and contig/scaffold-level draft. EndHiC is designed for the chromosome-level assembly of any species with HiFi and Hi-C data, and prior genome size and chromosome number are not necessary. By the way, you need to check the contig or scaffold N50/N90 size, since EndHiC works best with large contigs.
Sen Wang
Hi Sen: Thank you for responding. Below are my bbstats genome-assembly metrics from our HiFiasm assembly. You can see the contig lengths in the table. Also, would it be better to use the full contig assembly from HIFIasm or one of the haplotype-phased blocks? Thank you. Andreas
Main genome scaffold total: 1281 Main genome contig total: 1281 Main genome scaffold sequence total: 6131.895 MB Main genome contig sequence total: 6131.895 MB 0.000% gap Main genome scaffold N/L50: 58/28.024 MB Main genome contig N/L50: 58/28.024 MB Main genome scaffold N/L90: 31/43.668 MB Main genome contig N/L90: 31/43.668 MB Max scaffold length: 121.696 MB Max contig length: 121.696 MB Number of scaffolds > 50 KB: 867 % main genome in scaffolds > 50 KB: 99.79%
Minimum Number Number Total Total Scaffold Scaffold of of Scaffold Contig Contig Length Scaffolds Contigs Length Length Coverage -------- -------------- -------------- -------------- -------------- -------- All 1,281 1,281 6,131,894,624 6,131,894,624 100.00% 500 1,281 1,281 6,131,894,624 6,131,894,624 100.00% 1 KB 1,280 1,280 6,131,893,704 6,131,893,704 100.00% 2.5 KB 1,279 1,279 6,131,891,897 6,131,891,897 100.00% 5 KB 1,278 1,278 6,131,888,419 6,131,888,419 100.00% 10 KB 1,276 1,276 6,131,877,782 6,131,877,782 100.00% 25 KB 1,169 1,169 6,129,615,205 6,129,615,205 100.00% 50 KB 867 867 6,119,277,438 6,119,277,438 100.00% 100 KB 754 754 6,111,568,205 6,111,568,205 100.00% 250 KB 631 631 6,090,699,183 6,090,699,183 100.00% 500 KB 532 532 6,055,877,007 6,055,877,007 100.00% 1 MB 442 442 5,991,897,596 5,991,897,596 100.00% 2.5 MB 342 342 5,828,361,974 5,828,361,974 100.00% 5 MB 252 252 5,499,084,476 5,499,084,476 100.00% 10 MB 156 156 4,800,604,825 4,800,604,825 100.00% 25 MB 66 66 3,282,147,106 3,282,147,106 100.00% 50 MB 26 26 1,920,521,017 1,920,521,017 100.00% 100 MB 4 4 430,271,999 430,271,999 100.00%
Hi Andreas: The assembly continuity is very good, and I think EndHiC work well for this genome. The assembly sequences directly from hifiasm are "contigs" but not "scaffolds", because a contig can not contain gaps while a scaffold normally contains gaps jointing several contigs by correct order and orientation. Hope your work goes well! Sen
Thanks again, Sen. I had a word slip in the first message. I hope this works for us. I am curious, what is the largest genome you have or others have scaffolded with EndHiC that you know of? We haven't had very good success with other scaffolding programs. Thanks. Andreas
For a diploid plant genome of ~ 7Gb, I have ever used EndHiC to complete the chromosome-level assembly. In my opinion, large genome size is not a chanllenge for a scaffolding program, and what matters is the genome complexity, like tandem repeat, chromatin conformation, etc. Sen
Hi: I am studying a non-model diploid mammal species with a large genome size (~6GB). I have 30X Hifi data, as well as Hi-C data from Dovetail Genomics using their Chicago libraries. I have made an assembly in HiFiASM with the HiFi data. I would like to use EndHiC and am trying to use Hi-C Pro to generate input files for EndHiC. Hi-C Pro wants a table file of chromosome sizes. I don't have chromosome size information for my species. Can I create a table of scaffold lengths from my HiFiasm assembly? Or do these methods only really work on species with already known genome information? This question might be more appropriate for the Hi-C Pro folks, but I thought I would also check here. Thanks in advance. best, Andreas