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Hi Haoyu,
This is related to #55, where I noticed that hifiasm was not correctly identifying the heterozygous and homozygous peaks. The animal that I'm working with is very heterozygous (>4%), so t…
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I want to assembly a genome from paired-end Illumina short reads (2x150). I realize this will be fairly fragmented, for my purposes that is ok for now. I just need to estimate the system resources to …
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Hello,
I am getting an error in layout_unitigs.py.
[tska223@dtn HiC]$ python /opt/SALSA/layout_unitigs.py -x abc -l scaffold/contig_links_scaled_sorted_iteration_1 -c 1000 -i 1 -d scaffold
…
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Hi,
When running MBG with K-mer=301, the job finishes successfully. However, I have been running into this error when running MBG with higher K-mer sizes (I've tried both k=401 and k=501):
```…
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I assembled a genome using HICANU software, now which FASTA file should I use for the next HIC mount?
ccs_asm.contigs.fasta
ccs_asm.unassembled.fasta
ccs_asm.unitigs.fasta
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I'm trying to work out how SALSA will deal with large bubbles in unphased diploid genome graphs. The SALSA paper notes that heterozygous genome assemblies should be de-duplicated before scaffolding i.…
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Hi guys,
I'm experiencing an issue for running the whole genome prediction model, only when using the --lineage-clusters option. I'm runnning the following code:
`pyseer --kmers ../../2021_06_08…
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Hi John,
I am getting an 'Illegal instruction (core dumped)' error on a fresh install of unitig-caller under conda 4.9.2 (python3). I confirmed on a CLIMB instance. I have a working environment fr…
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Hello Pierre,
I use the bioconda discoSNP++ version (2.5.4).
I found a bug in the given positions of the SNPs in the vcf output of discoSNP++ (except if I missunderstood something).
When ther…
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Not sure if this matters, catlas still built
```
rule bcalm_catlas_prepare_input:
input: rgnv_nbhd_diginorm_hardtrim2_k31/bcalm.unitigs.fa, rgnv_nbhd_diginorm_hardtrim2_k31/bcalm.unitigs.pre…