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Dear all:
I want to identify variation between two similar genome, but when I use Mummer4 it use almost more than 1000Gb RAM, our linux server can't run with it, the larger one genome size is abo…
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We have a new `--chunk` parameter to split the ILP corpus for faster parallel computing.
However, when the chunk size is too large concerning the number of input genomes, RIBAP crashes. E.g., I tr…
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It can take several hours to calculate and store metadata for large numbers of genomes. This may be due to the size of the database transaction. Can this be improved? Is it simple enough to do this in…
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Good day,
I'm currently working on the assembly of a large mammalian genome. I would like to perform the reference-assisted scaffolding using ragout. However, I cannot run progressive cactus on the g…
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When running winnowmap, the -I option is not recognized.
e.g. after generating the repetitive_k15.txt with meryl:
`winnowmap -W repetitive_k15.txt -a -x map-pb -Y -L --eqx --cs -I 32G ref.fa.gz re…
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Hi Matt,
Thanks for InStrain, it's a great piece of software! I'm no bioinformatician, but I've been trying to wrap my head around how the profile pipeline calculates breadth on a scaffold and geno…
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I ran mosdepth twice on the same WES samples and got different coverage values. I used the same exome intervals bed file and reference genome build (hg38). There version of mosdepth used was different…
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Hi!
I have used hifiasm(0.14-r312) on HiFi-reads only to assemble an allotetraploid plant(coverage ~50x). The options : -t48 -l0 were used in this assembly. All output files were generated successful…
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Hello,
I had attempted to run DRUMMER using the exome mode across my genome reads as follows:
```
mkdir -p /rhea/scratch/brussel/vo/000/bvo00030/vsc11010/results_mouse_debugging/drummer/
mkd…
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When using `datasets` to download a large collection of genomes, many of the associated ```.fna``` files are silently truncated. I was fortunate in that: 1) a few of the files were truncated so that…