Xiaofei Zeng

Sorry for the delay. I'm quite busy these days. Your contact heatmap shows that there are still many errors in the contig assignment, as well as the ordering and orientation....

Here are two examples of *S. spontaneum* Np-X (sugarcane) and *C. sinensis* Tieguanyin (tea plant):  

Hi @chenzixi07, **1)** In theory, primary unitigs (`p_utg`) have no phasing errors if generated correctly. However, they are typically much shorter than haplotype-phased contigs (`hap*.p_ctg`). If hifiasm is able to...

**1)** Although the second haplotype assembly is slightly shorter, you can try using it. **2)** How did you estimate the genome size? You can veritfy this based on the k-mer...

> We estimated the genome size by both FCM and short-reads/long-reads genome survey (although the result is...weird.) What method did you use for the genome survey? Generally, I do not...

> I tried to use the concatenated hap*.p_ctg files as the reference genome. After bwa mapping, the size of the bam file is 371G, but the filtered bam is only...

Maybe the Hi-C mode of hifiasm assembled too many identical sequences that are not in the primary unitigs, which can lead to fewer effective Hi-C reads after filtering. You can...

Hi @socialhang, I have a plan to support Pore-C data, but it is not a high priority at the moment. I haven't conducted any tests on Pore-C data yet, so...

Hi @socialhang, I have conducted an experiment on the test data of https://github.com/epi2me-labs/wf-pore-c. You can try the following steps with your own FASTA and FASTQ files: (1) Execute the wf-pore-c...

Hi @socialhang, You could try it. It seems that `falign` can produce pairwise SAM files that compatible with SALSA2 using the command `sam2salsa2` in `u4falign`. Best, Xiaofei