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I've tried herro on one of our read sets (with R9.4.1 model) and when I compare the reads before and after correction, by aligning them on the reference assembly, the result is very convincing (very f…
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```
Then, the circular contigs were left alone, and each tangled “circle” was re-assembled by Hifiasm-meta with default parameters, using the fragmental contigs that constructed the “circle” as input…
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My circlator (Circlator version: 1.5.5) run with the following command was running for 3 days and then stopped and never continued. Here is the last part of the log file:
Command:
```
circlator a…
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HapHiC is working very well so far, and now we would like to fine-tune the scaffolding (looking into more of the options, and comparing different input versions).
**My question:** Is it possible t…
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I have a homozygous genome. so it is suggested to run the assembly with -l0. When i run the assembly with purging as 0 the N50 value is 15mb. but whwn i run the assembly with purging as 2 , the N50 va…
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Thank you for providing herro.
I've tested it on four ONT datasets one of which is public.
The number reads and nucleotides after correction are very variable, ranging in my case from 2 to 20% for…
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I didn't get any results after entering the command. What could be the problem?
Could you possibly spare some time to take a look for me, please? I would greatly appreciate your help. The command I…
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For assembly of metagenomic samples with HiFi reads, I ran hifiasm-meta with default parameters. The command line was as follow:
hifiasm_meta -t 32 -o asm hifi_reads.fastq.gz
But the process was e…
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I tried istalling it with conda and stand alone but still it didnot work .
TRASH_run.sh: 3: Bad substitution
/vol/pac/Software/TRASH
TRASH will be run with /vol/pac/New/old_TRASH_results/TRASH/…
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### Description of the bug
Hifiasm has built-in purging of haplotigs and seem to claim that purge_dups is too aggressive in purging (https://github.com/chhylp123/hifiasm/issues/162). Have you done c…