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There is now BLAST XML v2 as of BLAST+ 2.2.31, which will most likely become a second datatype in Galaxy (especially if it has to be a container style datatype with multiple files due to the use of XI…
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BLAST+ can be used with the NCBI taxonomy files, particularly for building databases - can we tie this into Galaxy's ``ncbi_taxonomy.loc`` allowing versioning vs the current behaviour of implicitly us…
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#### what is multiPhATE
[multiPhate](https://github.com/carolzhou/multiPhATE)
* fully automated computational pipeline for identifying and annotating phage genes in genome sequence
* controled by a…
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Hi, while i was trying to run ncbi blast in apscale, in some of the fasta subsets i keep encountering this error. I've tried to exclude uncultured sample sequences during blast search and downloaded x…
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Hello!
I want to analyse my samples against 16S NCBI database, which I downloaded previously, but when I tried the last step, function predict(), its takes 5 days without results. Do you know what…
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> > The NCBI is now making a new version of the BLAST XML available for
> > testing. Read about the changes and how to access BLAST results using
> > the new XML at ftp://ftp.ncbi.nlm.nih.gov/blast/d…
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To support unaligned NCBI datasets (the vast majority):
(1) Extract target region from reference sequence and create blast db from it
(2) Magic-BLAST dataset against region
Example:
```
#!/us…
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## Summary:
Should we bother recording `makeblastdb` version numbers/parameters in the database, for reproducibility. As noted in #90 - I'm ambivalent about recording `makeblastdb` version/paramete…
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Hi,
I am not 100% sure that I am not misreading this, but in:
https://github.com/CVUA-RRW/FooDMe/blob/master/ressources/fetch_nt_blast.sh
it reads as if the script downloads directly out of htt…
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Reported by a user:
```
$ blastx \
-db /blastDB/uniref90 -query genome.cds \
-out Genome_UR90_02062018.cds.tsv 1>blastx.log 2>blastx.err \
-outfmt "6 qseqid sseqid slen length pident …