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Hello, I am trying to extract COI genes from raw Illumina sequences of cestodes to try and ID the hosts. I am using the cestodes as a proof of concept but would eventually like to try it with whole ge…
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I tried to align whole genome reads (hg19) generated from pbsim using GraphAligner.
However, the program crashed when building minimizer seeder from the graph.
This is the error message that I got:…
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Hi
I've been running Cactus on 3 different Barley genomes (planning to scale up to more genomes later). I've been running each job to create alignments of each chromosome from 1 to 7. I'm breaking …
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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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Is reveal capable of generating whole genome alignments for multi-gigabase genomes?
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Dear Authors,
Thank you for making ptACR available. I was reading the article, and wondering if it is appropriate to run it on SNP only alignment rather than on a whole genome alignment.
Thank y…
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I hacked together a method based on the minimap2 alignment strategy. The basic idea right now is that after producing whole genome alignments via minimap, one can use the paftools liftover command to …
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Adding ska to our phylogenetics inference offerings would provide an alternative reference-free phylogenetics analysis tool in addition to kSNP3. It could also be used for creating whole genome alignm…
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Hello,
I’ve been admiring the chromosome collinearity images produced by the ` jcvi.graphics.karyotype` module; they are indeed very beautiful. However, it seems that this module is designed prima…
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First of all, thanks for your wonderful tool ! It's really helpful for my research !
I build a vg graph from a collection of virus strain genomes (~10000bp per genome, some are very similar) , and …