Stephen Nayfach

ModuleNotFoundError: No module named 'edlib'

1

I installed the program using: `conda install -c bioconda badread -y` But got the error: > Traceback (most recent call last): > File "/global/homes/s/snayfach/.conda/envs/flye/bin/badread", line 10, in > sys.exit(main()) >...

CD-HIT para for SLURM

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I'd like to run the cd-hit-para.pl script on a SLURM cluster? Is this possible? Is there any way to manually split up the task to be distributed over a large...

Recommendation for multiple genome alignment

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Do the authors have any recommendations for a tool to generate fast bacterial genome alignments that can be input to snp-sites?

Option for max hits per query

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Would it be easy to add a flag to report only the top n hits per query sequence? This would enable users to get the most similar genome in their...

Save sketches for reuse

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When the reference is large, a lot of time is spent during the sketch stage. Is it possible (currently or in the future) to save and reuse sketches across multiple...

Could you please comment on what data was used for model training. Thank you

I'm running the command: `mmseqs easy-taxonomy taxdb output tmp -e 1e-5 -s 6 --blacklist --tax-lineage 1 --majority 0.75` However many of the taxonomy results have

Obtaining diversity estimate

3

Thanks for the great documentation and software design. Installation and running was super easy. One question - how to I obtain the nonpareil sequence diversity estimate? I may have missed...

Problems handling errors in reference genomes

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I'm trying to run PHIST on a single viral contig vs a large database of gzipped bacterial genomes. The program finishes without errors, but stops after the first ~715 reference...

I'm interested in performing ultra-fast classification of metagenomic reads against a database that contains a single pangenome (thousands of genomes of the same species). My goal is to identify the...