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We have previously discussed adding metagenomics compatibility by running fly in meta mode and doing genome binning.
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Hi, I have HiFi reads, ONT-reads, HiC reads, and parents illumina short reads. So, I ran hifiasm with trio-binning mode to conduct haplotype assembly with the code 'hifiasm -o prefix.asm -t 32 --ul on…
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I mentioned recently that arc view would sort of put pressure on our code to optimize other parts of our system, since arc track is often useful to view in a zoomed out view. One of those parts of the…
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## Is your feature request related to a problem? Please describe
At the moment there is an input option to use only [short reads](https://nf-co.re/mag/usage#direct-fastq-input-short-reads-only).
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Hey,
I have been working on metagenomic data that comprises yeast and bacteria in the microbiome . We did a WGS on our samples in Illumina platform. From the sequencing results, I'm able to resolve…
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I assume that npScarf is designed for Single species bacteria. Anyhow, I want to check how it works for my bacteria in metagenomics sample. With Illumina MISEQ data, I did the assembly with SPADES …
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I ran hifiasm (trio) on 3 SMRT cells of diploid CCS data for a F1 hybrid on which I have parental Illumina data. I expect two haplotypes around 2.8gb, however, the size of the haplotypes is drasticall…
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QC'ed the reads with illumina-utils (specifically iu-filter-quality-minoche and iu-merge pairs in two different attempts), performed preliminary binning with MegaHIT; feedback at the end was as in the…
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Hello, professor
I want to know the differences bewteen trio modle and HiC model? Is there a difference in the detection of structural variation? Will the trio model completely split the genome into …
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Hello @chhylp123
I used hifiasm in trio binning mode using Illumina reads from the parents and HiFi reads from the hybrid. The resulting assemblies (hap1 and hap2) have high duplication levels and…