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I use a contig.fa (by Hifiasm) and a BED file (by Chromap)
yahs version:1.2a.2
This is the problem
`yahs: cov.c:474: calc_cov_norms: Assertion `k == div_ceil(p1, window)' failed.
Aborted (core dum…
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yahs version: v1.2a.2
chromap version: v0.2.4-r467
hello, if I use chromap to generate both a `.sam` and the `.bed` file from the same Hi-C dataset, then `yahs` only works with the .`bam` file.
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Hi, Thank you for creating and maintaining YaHS. I would like to ask question regarding the following:
After I assembled the genome using yahs, I purged the assembly using purge_dups. I would like to…
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Hi,
I have assembled the highly heterozygous and repetitive genome of a plant using HiFi and Omni-C, running hifiasm to generate a phased diploid assembly. I then processed the omni-c reads through…
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I have scaffolded an assembly using yahs and am trying to manually curate it in JBAT, but I am running into issues using juicer_tools pre. I know that this tool is not part of yahs but since I'm runni…
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I'm working on scaffolding a HiCanu assembly for a shark species that has had duplicates purged. It was assembled with ~45x PacBio Hifi (Median length: 13,710 bp; Mean length: 13,590 bp; Max. length: …
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Hi Yahs Team,
java -Xmx32G -jar juicer_tools.2.20.00.jar post -o output abdullah_manual_out_JBAT.review.assembly out_JBAT.liftover.agp yahs.out_scaffolds_final.fa
WARNING: sun.reflect.Reflectio…
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Dear yahs developers,
I'm trying to scaffold a de novo assembly following your pipeline.
I'm at the step "Generate Hi-C contact maps" and trying to run the first command:
/software/yahs/ju…
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[I::main] dump hic links (BAM) to binary file yahs.out.bin
[I::dump_links_from_bam_file] 1 million records processed, 0 read pairs
[I::dump_links_from_bam_file] 2 million records processed, 0 read …
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HELLO.
my out.JBAT.log file generated is empty.
(java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part