Tanger Zhang

Hi @zhxh233 , I do not think the link you posted could solve the assembly of sex chromosomes. If you are working on the sex chromosomes, I suggest you can...

Hi @baishengjun It may be caused by Hi-C scaffolding but also may resulted from the genetic map. According to my experience, the genetic map sometimes suffers from genotyping errors, leading...

Based on our experience, the enormous chromosome size is likely due to chimeric contig assemblies. I suggest correcting these contigs before scaffolding. You can use the ALLHiC_corrector function to achieve...

Hi @phil622 It happens when the Hi-C is far from high-quality. Did you use HiC-Pro to check the unique mapping and valid rate?

Hi @phil622 Yes, I think the hic quality is likely an issue resulting in this situation.

How about the valid rate?

Hi @phil622 Even though the valid rate is 70%, I still have doubt that the valid reads are not enough to link the contigs into chromosomes. I would suggest to...

Sure! ALLHiC is definitely applicable to simple genomes. I've uploaded a file, namely ALLHiC_pip.sh (https://github.com/tangerzhang/ALLHiC/blob/master/bin/ALLHiC_pip.sh), which wraps a couple of functions including reads mapping, correction, partition, optimize, build and plot....

Hi @pjx1990 ALLHiC can anchor contigs onto chromosomes if the number of chromosomes is given. The new pipeline I just uploaded includes correction of contigs and therefore may have a...

Thanks for mentioning us. The ```ParaFly``` comes from trinity package (https://github.com/trinityrnaseq/trinityrnaseq) and it is used for parallel running of dozens of command lines. I will add an update README shortly.