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Is it possible for someone to give me the strict definitions for the 'Best Hit' and 'Weight' variables seen in the Pathoscope results? I can't find them in the docs or anywhere. Thank you, Joe.
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Hi, I am wondering what the memory requirements are for searching against very large database (500GB - 1 TB)? On the query side I can do the splitting but splitting the database would produce less tha…
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I've just been reading Kraken's documentation, and am curious why fungi aren't included in the standard Kraken database?
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Hey Jie and Nathan,
Maybe I entirely missed it, in which case I am very sorry to bother you, but could you make the exact data subset from "RefSeq virus and prokaryotic genomes sequenced from before …
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Installed ROARY on Biolinux 8
Roary installation checked using
roary -a
Everything is looking fine
I ran the following command
roary -e -n --mafft -p 8 -t 1 -r -f foldername .*gff
After analy…
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```
[kb219@compute-a-16-71 ~]$ prophyle download viruses
[prophyle] 2017-11-13 23:31:08 Downloading "viruses" started
[prophyle] 2017-11-13 23:31:08 Checking library 'viruses' in '/home/kb219/proph…
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use command:
```
./bin/fusioncatcher-build -g homo_sapiens -o /haplox/users/wenger/pipe/RNA/fusion_human
error :
Downloading the viral genomes from NCBI server!
230 Anonymous access granted, r…
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Hi
I am using Prokka to annotate a set of genomes using a custom nucleotide hmm database I built using hmmer (hmmbuild). I used the following pipeline to do this
1. Create hmms for each gene using…
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Hi Derrick,
Can you please help on the following issue:
bhaley@NextSeq-Server:/**$ ./kraken-build --standard --db /**/kraken_DB
Found jellyfish v1.1.11
--2016-03-08 17:40:58-- ftp://ftp.ncbi.nih.g…
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I am doing virus mapping to get genomes. I dont get why I changed the reference of virus genome, snippy returned different snps.consensus.fa with about >30 snps differ. Is that means the method is wor…