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Suggestion from @drtamermansour: in a single pass, write count tables to N files (one for each band) in a single pass. Then running `kevlar find` in N bands would not require N passes over the entire …
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Hello, I have a hypermemory problem:
The error message is as follows:
==============================================================
[M::ha_hist_line] rest: ***************************************…
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## Expected Behaviour
Unknown
## Current Behaviour
I am trying to re-create the clustered nr database currently featured on the BLAST site. The cluster step appears to stall after merging the…
cef61 updated
2 weeks ago
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Hi,
when I try to run vargeno on the same data linked in my previous issue (https://github.com/medvedevgroup/vargeno/issues/2), it crashes during the geno step.
This is the output of `vargeno inde…
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Results seem to be okay, so there clearly are valid k-mers. This appears to be only an issue with estimating the set size of the k-mer pool, and an inaccurate warning resulting from it.
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Would it be possible in `compare` or `index` to include a TF-IDF-style step that reweighted the k-mers based on their "rareness" in the corpus? i.e. k-mers that are ubiquitous would receive a lower we…
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When running `StreamingQueryDNADatabase.py`, in reality, we need only the K-mers in the sample that exist in the training database sketches. As such, it's possible to:
1. Dump all the training databa…
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I have been trying to assemble a 10Mb genome with uncorrected nanopore data (3-4 chromosomes expected). We have a lot of data, is that the reason Flye fails at the end?
[2019-06-22 11:00:05] INFO: …
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Currently, `sencha translate` uses a simple match of whether 100% of the k-mers from the reading frame, match the reference proteome. But a "Franken k-mer" situation can happen where the reading frame…
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Hi, I'm trying to run the flow via snakemake (snakemake --cores all --use-conda ) but I get this error.
https://raw.githubusercontent.com/akcorut/kGWASflow/v1.3.0/workflow/rules/common.smk:98: Sy…