Tanger Zhang

As far as I know, you can get two haplotype assemblies at contig-level from hifiasm if you specify the parameters --h1 and --h2, which take the Hi-C data as inputs....

Hi @dpaudel You can modify the script in Lines 53 and 65, and change the string 'Name=' to 'ID=' It is supposed to solve this problem. Thanks!

Hi @HMPNK, I am not aware that minimap2 is suitable for Illumina reads mapping. Actually, bwa mapping is a bit slow, however, you can split the big fastq files into...

Yes, It should be totally OK to merge the hap1.p_ctg.fa and hap2.p_ctg.fa and run ALLHiC for haplotype phasing. Alternatively, you can also use p_utg.fa for ALLHiC phasing if you do...

Hi @rillaxy I have very limited experience with juice box adjustment. And I have no idea if it works on a 5.6-Gb genome. A hic plot and dot plot analysis...

Hi @Johnsonzcode This situation happens when the initial assembly has many chimeric contigs. You can first correct the contigs using 3D-DNA or ALLHiC_corrector. If you are using ALLHiC_corrector, the following...

Yes, you are right. If you skip the filtering step, you can use ```sample.bwa_mem.REduced.paired_only.bam``` instead. Alternatively, if you are working on a genome with a high level of repetitive sequences,...

> Sorry for reopening it. When I try to correct contigs, mapping HiC reads to draft assembly confused me, in which `bwa mem`: > > 1. I am not sure...

ALLHiC_correct takes bwa-mem with paired-end reads alignment but we have not tested it on bowtie2 with single-end mode. Please let us know if it works on bowtie2 mapping. Otherwise, we...

Yes, It should be OK to generate the phased assembly using ALLHiC pipeline.