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Hi,
I'm new to using the bacLIFE pipeline for analyzing genomes. I've been encountering various issues, including errors during the big_scape, EGGnog, and antismash steps.
After trying to troubl…
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Hi there,
I'm running a pangenome analyisis on 20 bacterial strains using roary version 3.13, on a server running CentOS 7.
I want to get the unique genes present in only one of those 20 strains b…
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Hello dear author, it's exciting to find this new tool!
I've been following Mellisa but gave up due to the lack of detailed annotation of genome features, could you please give a brief suggestion wh…
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Hi,
When I use Rscript I met a problem:
```
$Rscript ./bin/clustering_chrs.R distictive_kmer_and_counts cluster_center.pdf dendrogram.pdf
Loading required package: ggplot2
Welcome! Want to lear…
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I am trying to use your software GI-cluster to help identify genomic Islands in my genomes. I notice when it runs the r program it get stuck on “cluster assignment” for a long time.
Can you help m…
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Hello, thank you very much for your SubPhaser software, which is very useful for genotyping. I used HIFI and HIC to assemble the genome of Fragaria x ananassa but I do not know the homology of the 28 …
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# Binning with CONCOCT
What makes CONCOCT an unsupervised binner is that it bins based on the characteristics of the sequences (sequence composition) and coverage information. Tetranucleotide freque…
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## Summary
MiXCR performs an alignment as well as an assembly step during its process of identifying clonotypes. During assembly, a clustering method is utilized to attempt to overcome PCR and sequen…
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Hi Isaac,
I'm running ipyrad [v.0.9.90] with maximum memory allocation (184G), 48 threads, and with the following (relevant) params:
```
~/all_trimmed_reads/*.fq ## [4] [s…
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Hi! Thanks for all of your work building SICER. It's our peak caller of choice, especially for broad domains!
I occasionally run into an error in the step: "Determining the score threshold from rando…