Issue about partition result

[YuChrming]

dear professor, I was assembling a triploid genome.The input of allhic is from hifiasm, *.asm.p_utg.fa which is without "bubble". Runing the partition step, weird results were found. ALLHiC_partition -b prunning.bam -r *.asm.p_utg.fa -e AAGCTT -k 3 The results are identical either I setting the parameter 3 or 17 , why? Cluster result show that nearly all the contigs(3300+) devided in one group, while residues were in 16 groups and less than 200 contigs in total.Is it normal? Thank and expect your response!

[tangerzhang]

Hi @YuChrming , I guess you are working to assemble a monoploid genome of the triploid species. If so, could you please try ALLHiC wrapped scripts for simple diploid genome scaffolding (https://github.com/tangerzhang/ALLHiC/blob/master/bin/ALLHiC_pip.sh). This pipeline contains correction of chimeric contigs, which are quite helpful for genome scaffolding based on our experience. Alternatively, you may also try a new Hi-C scaffolding tool (https://github.com/fanagislab/EndHiC) developed by my colleague. The new pipeline is specifically designed for contig assembly with extremely long N50, typically for HiFi assemblies. This strategy does not rely on the correction of chimeric contigs.

[YuChrming]

dear professor, I am really uncomprehending the "build" step. Usage: ALLHiC_build draft.asm.fasta Input file: draft.asm.fasta - contig-level assmbly How could I convert tour format to fasta sequences and agp location file? After all, it isn't used in command. And if I want to regard one group as one complete chromosome.What should I do? Thank a lot!

[ChenDepp]

hi when i running partition step, find it can't get result. The report message is as follows: