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hi ,dear author. when i use this tool to assemble my genome. first,i use the mecat2, and then i use pilion to polish, then use purge-haplotig, finalla use allhic, the survey genome size is 450M, and …
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Hello,
My Hi-C data was obtained using enzyme DpnII. However, AllHiC only has two enzyme options, such as -e : enzyme_sites (HindIII: AAGCTT; MboI: GATC). How can I set up the enzyme sites or I do n…
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Report a problem about mitochondrial genome inserted in to chromosome by ALLHIC. So the mitochondrial genome should be excluded from the fasta file for HIC assemble.
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Dear Dr. Zhang,
I have tried `ALLHIC` to scaffolds our genome by HiC data. We skipped `ALLHIC_prune` and `ALLHIC rescue` steps since our genome is a diploid genome.
For the `ALLHiC_partition` s…
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Hi Xingtan,
thanks for providing the wiki on ALLHiC.
I would like to run AllHiC with the example data you provided at ftp://59.79.232.12/. But it seems the ftp is not working (that I cannot get …
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I have a low heterozygous and diploid insect genome of about 480m. I notice ALLHIC is nearly the only HIC assembly tool maintained well. So I want to try ALLHIC to finish my assembly. The question is…
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Hello,
I was wondering if ALLHiC supports libraries generated using DNASE as the fragmenting enzyme?
If so, what should be input for the enzyme parameters during the filtering and partitioning step …
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Hi,
when I used test data to test the ALLMAP, and I am sure install all the python modules, but it does not work. The error log is following:
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Traceback (mo…
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Hej,
Could you share more details on how you ran Falcon-Phase on Proximo scaffolds (as mentioned in preprint).
Did you rename scaffolds and matching Phase 1 haplotigs in Falcon-Unzip style?
Wer…
iggyB updated
4 years ago
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Hi, @tanghaibao and @tangerzhang ,
Thanks for developing ALLHiC, a tool in urgent need and handy to use.
From your expertise, could you please kindly provide some advice about my assembly workfl…