User: kcamnairb

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kcamnairb40
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Posts by kcamnairb

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Whole-genome alignment of two or more bacterial genomes - find structural varian
... [NucDiff][1] looks interesting. I haven't been able to try it yet, but I know it can output a vcf. [1]: https://github.com/uio-cels/NucDiff ...
written 4 months ago by kcamnairb40
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Comment: C: What do Ns represent in a SPAdes assembly from single-end reads?
... There are 8 stretches of Ns in the assembly. Some of them are up to 512 bp, which is longer than the read length. ...
written 6 months ago by kcamnairb40
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What do Ns represent in a SPAdes assembly from single-end reads?
... The fungal genome assembly I've done using SPAdes with single-end reads has stretches of Ns present. I would expect this with paired end reads but I'm not sure what they represent when the assembly is done with single-end reads. The spades options I used were --iontorrent and --careful. Do these N's ...
assembly spades written 6 months ago by kcamnairb40 • updated 6 months ago by lieven.sterck2.2k
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Comment: C: Training Augustus for Maker
... I have run BUSCO with the "--long" option and it seemed to have completed successfully, but I don't see where the optimized augustus metaparameters are stored. I have looked in the augustus config directory and the BUSCO output directory. Is there somewhere else it is placed? ...
written 23 months ago by kcamnairb40
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Comment: C: ABySS syntax for reads split across two lanes
... Thanks, I'll try concatenating the reads. I actually have two libraries, so I think pooling libraries across multiple lanes is supposed to reduce any lane bias. ...
written 2.8 years ago by kcamnairb40
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ABySS syntax for reads split across two lanes
... Hi, I have a paired end library that was split among two sequencing lanes. The left and right reads are in separate files so I have a total of 4 files for each library. How would I specify this library in abyss, or do I need to concatenate the reads from the two lanes? For example, would this be pro ...
assembly abyss written 2.8 years ago by kcamnairb40 • updated 2.8 years ago by benv700
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Looking for software for Interproscan domain visualization
... Hi, I'm looking for software that would display protein domains identified by interproscan in a graphical form so that I could display it alongside a tree. I found a site called TreeDomViewer that looks like it would do what I'm looking for but it seems to be down. Are there any other similar progra ...
interproscan alignment domain visualization written 3.0 years ago by kcamnairb40 • updated 3.0 years ago by Biostar ♦♦ 20
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Answer: A: Post Genome Assembly
... There doesn't seem to be a publication available for this software yet, but I've found Medusa to be very useful: https://github.com/combogenomics/medusa It seems like many of the other scaffolding tools require paired-end reads or are designed for prokaryote genomes. ...
written 3.4 years ago by kcamnairb40

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Scholar 4 months ago, created an answer that has been accepted. For A: Whole-genome alignment of two or more bacterial genomes - find structural varian

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