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Hello,
I have a project that requires alignment of WGS Illumina data on specific regions of the hg38 reference genome. I want to speed up the whole process, so I do not have to map my reads to the …
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Dear author, multiz is a very useful software. However, at present, I need to merge more genomes, according to the pairwise merger speed is too slow, is there any way to improve the merger speed? Than…
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jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkag…
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Hello,
I have a question for you. If I want to do whole genome alignment between two genomes and apply the target[multiple] in the command line, does it mean that I can parallel run the lastz? Also,…
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I tried running MUM&Co on several query-reference pairs. In several occasions, I got the error:
> Matching query and reference chromosomes
>
> awk: cmd. line:1: fatal: division by zero attempted…
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Hi
In the Cactus paper (https://www.biorxiv.org/content/10.1101/730531v3) it mentions that it expects the input genomes to be soft-masked. I was wondering how Cactus treats the soft-masked regions.…
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Hi Glenn!
I'm currently running `cactus-hal2maf` on a new alignment I've generated using Cactus v2.8.2. I'm running Cactus as a singularity image on a computing cluster. Anyways, I have an alignmen…
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Hi,
I have been using minimap2 for many genome to genome alignments and I have noticed an odd pattern.
If I take a large genome like a human genome and align (paf output) the whole chromosomes …
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# OGS remapping
- [ ] request whole-genome alignment
- [ ] Set up data directories and get data
- [ ] run remap-gff3
# manual annotation remapping
- [ ] request whole-genome alignment
- [ …
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Hi,
I'm new to this and I want to construct a recombination free core SNP phylogenetic tree using snippy and gubbins.
I'm confused because core.aln is a core SNP alignment file and core.full.aln is…