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We are trying to align ~5000 bacterial genomes and are finding a number of issues. One of them happens on calling getLongestPath
The problem is due to the default limit on recursion in python, whic…
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Hi, I am wondering whether Bracken factors the size of bacterial genome into the calculation of relative abundance. If having a defined consortium consisting of a few of known bacteria with a large va…
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We tried running the SOAPdenovo_array.sh script using 30 .fq files of total size 557GB as input and a reference genome with a total size of approximately 17GB.
The SOAPdenovo_array.sh script requires…
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Hi,
Great work!
Do you think that, if trained, Tiberius will provide equally good results for other groups of organisms other than mammals? Such as in large invertebrate genomes?
Also, do yo…
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**Describe the bug**
I'm running HMMRATAC on several plant genomes which vary greatly in size. HMMRATAC fails when running on the largest genomes that require a .csi index. It produces the following …
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Hello! We have been having an issue running souporcell with either a large genome or matching supertranscriptome. Our scripts for the full pipeline run for over 7 days and then run out of time on our …
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![transformed_log_plot](https://github.com/user-attachments/assets/fb237975-232e-4bcd-9518-a817c99c7377)
[summary.txt](https://github.com/user-attachments/files/17161668/summary.txt)
Thank you so …
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Analysis of simulated validation data by the CARD team (unpublished) revealed that Prodigal undercalls ORFs when the _-split_prodigal_jobs_ option is used. This was particularly noticeable in a _Acine…
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For large eukaryotic genomes, the file overlap.paf may be very large. I think, VeChat can be optimized in two ways to deal with this:
1) Instead of making overlap.paf, it can make overlap.paf.gz . Th…
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gridss conda installation
jar file 2.13.2-gridss-jar-with-dependencies.jar
platform : Ubuntu 22
The code I ran
`gridss -t 20 -r ./reference/Ref/GRCh38.p14.genome.fa -j ~/tools/gridss-2.13.2-gri…