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Hello,
1) I am working with a non model organism (a diploid insect), thus we don't have any Closely related 'diploid' species. Can I still use ALLHIC ?
2) My contig assembly is quite good (4000 …
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Hi,
I tested ALLHiC and SALSA2 with a diploid genome assembly(19 + XY) that is built from linked-reads (Pseudohap 1 style) and shows around 35kb of contig N50. and I found that the outputs are way di…
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Thank you for developing f ALLHIC. When I use ALLHiC_partition function, no results were generated. Is something wrong? Looking forward to your help, thank you.
Extract function: calculate an empiri…
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Hi,
Thanks for developing this useful tool. I assembled two haplotypes from a diploid plant using the hifiasm tool with HiFi and HiC data. Now, I use HiC data to anchor two haplotypes. You mentioned …
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Dear Professor Zhang,
The species I study is an insect which has 36 chromosomes,and its genome size is 5.6Gb. The initial genome was mounted to 40 chromosomes using Allhic software(Because the size o…
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Hi, I am getting an error while running the ALLHiC_partition step. I skipped the Prune process. My command is ALLHiC_partition -b sample.clean.bam -r genome.polish.fasta -e AAGCTT -k 16
The running c…
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Hello,
I have assembled a tetraploid genome using hifiasm.
The size of *r_utg.gfa and *p_utg.gfa are consistent with all tetraploid genome size .
*bp.p_ctg.gfa is a little smaller than all…
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Hi @tangerzhang,
I am running allhic with a genome of size around 3 Gb, at a read coverage of 100x.
I observed super large sizes of intermediate files during pruning step, like below:
total …
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Hi, Prof. Zhang,
Recently, i have a dipolid geome (2n=12) project. And it has 1.7% heterozygosity. Fisrt, i removed redundant sequnces using purge_haplotigs. Then, these contigs were scaffolding u…
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hi,
when i run 'partition.pl -g Allele.gene.table -r draft.asm.fasta -b sample.clean.bam -d wrk_dir', the error is:Died at /data/software/ALLHiC/scripts/partition.pl line 59. Why is that？