Rebecca

After adjusting the parameters based on the information from the Hifiasm.log file, the issue of "phased assembly is much larger than the estimated genome size" still persists.

1

Hello, When assembling the genome of a species using HiFi data with hiFiasm, I encountered a peculiar situation. The genome size of my species is approximately 1.1 G. Following your...

How to get the unique matching path for each read

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Hi, Thanks for the clear documentation and awesome tool. I would like to get the unique matching path for each read.But through the following code, I saw that in the...

How to infer different species-level abundances based on strain-level abundances

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Hi! Thanks for the clear documentation and awesome tool. I have read your explanation about Strainscan, and it seems that it is used to analyze the abundance of each strain...

[BUG]For HiC data, the size of SAM files outputted using Chromap is much smaller compared to those from BWA-MEM

4

Thank you for providing such a useful tool . **Describe the bug** I have a set of HiC data and I would like to split it by chromosome. I aligned...

Thank you very much for providing such useful assembly software！ The hifiasm version I am using is 0.19.8-r603 I am trying to assemble a diploid genome, first using the following...

The process of polishing causes a significant decrease in genome size.

11

Hello, thank you for providing such a useful assembly software. I have a question and would like your help. After nextpolish polished my genome file, my genome size was reduced...

Thank you for developing ALLHIC. I did an HiC mount for the autotetraploid assembly I assembled according to the wiki, and there was no error, but when the result was...

Hello, thank you for providing such a useful software. Can I use sim3C to generate hic data that is disconnected according to the restriction site? Instead of 150bp data with...

Thank you for providing such a useful software. I used sim3C to simulate a hic data for my E. coli genome. Use the following code: `sim3C --profile mycom.txt -n 5000000...

Where to get detailed description of GFAse's computational methods？

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Hi, I am very interested in the methods of GFAse. I have carefully read your paper ‘Phased nanopore assembly with Shasta and modular graph phasing with GFAse’, but I don’t...