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Hi, I want to make sure that when I use smoove call for tumor/normal pairs.
Is there a requirement for the order of two bam files?
Which command is correct ?
The command is as follows:
`smoove ca…
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Hello author, I have a question about reference-free methods. Progressive Cactus is a reference-free multi-genome alignment, and it seems to be independent of the reference genome during the alignment…
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### Description of feature
For any steps requiring a reference, we should be passing it or using REF_CACHE.
---- Some notes from JIRA ticket TOLIT-1916 on this topic ----
For using CRAM with…
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Thank you for your effort on these tools, I am using EDTA (v2.2.1) to carry out de novo TE annotation. After I used EDTA output file `fasta.mod.EDTA.raw/LTR/.fasta.mod.pass.list` and `.fasta.mod.EDTA.…
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Hello,
No mention of having to use soft-masked vs unmasked FASTA genome as input for MirMachine, so I assume that an unmasked genome is OK? Can you confirm? TIA
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Please advise how to code the common option for scenario (4), if I only have the assembled .fna files to be targeted that are saved locally, not in NCBI.
Thank you!
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Hello,
I am working on plant species which is highly heterozygous and shows chromosomal aneuploidy. We have both 25× HiFi data and 50× HiC. Is it possible to generate a complete phased assembly u…
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I might have missed the information in the documentation, but I don't think there is a way to input a custom-made reference genome for the alignment step.
If I have well understood, the pipeline us…
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Hello,
I have a highly hybrid plant genome, jellyfish and genomescope is estimated to be 3.44G , 2.87% heterozygosity, but 4.57G in haifiasm assembly. I try to set the value of --hom-cov 24, he geno…