Moderator: Brian Bushnell
Brian Bushnell ♦ 17k
- Reputation:
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- Walnut Creek, USA
- Website:
- http://sourceforge.net...
- Last seen:
- 5 days, 1 hour ago
- Joined:
- 5 years, 2 months ago
- Email:
- b********@lbl.gov
I like to program in Java.
Posts by Brian Bushnell
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... Yes, catting would work; in addition to catting the files, you can also stream them to stdin:
cat *.fasta | sketch.sh in=stdin.fa onesketch out=xyz.sketch
That said, I'm not sure why you would want to make one sketch for thousands of fasta files. If you want one sketch per input file, with al ...
written 5 days ago by
Brian Bushnell ♦ 17k
• updated
5 days ago by
genomax ♦ 76k
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Comment:
C: viral genome assembly
... Tadpole seems to do a better job of assembling viruses than Spades. I won't guarantee that, but it seems to be generally true.
Viruses and hosts can share sequence. If you remove all sequences shared between the virus and host, it's likely that you will incur holes in your assembly, if you are tr ...
written 6 weeks ago by
Brian Bushnell ♦ 17k
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... BBDuk is a filter. At JGI we use it to remove reads with 31-mers corresponding to common ribosomal 31-mers, because some downstream tools like Trinity fail when there is an overload of rRNA reads.
Running BBDuk with common ribosomal kmers is good practice, but not ideal; the sensitivity and specif ...
written 6 weeks ago by
Brian Bushnell ♦ 17k
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... I just revised all of the fetch scripts in 38.61b which I released today. You should be able to do this:
Run fetchTaxonomy.sh
Then modify fetchNt.sh to change the line TAXPATH="auto" to point to wherever you downloaded the taxonomy data.
Then run fetchNt.sh.
That will give you nt which is not as ...
written 5 months ago by
Brian Bushnell ♦ 17k
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... OK, all servers are back up again!
RefSeq is the default server. You can specify: refseq, protein, nt, or ribo (aka silva). It will only connect to one server each time you run it. ...
written 5 months ago by
Brian Bushnell ♦ 17k
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... The important thing here is:
Query: scaffolds.drop_bacteria.fasta DB: RefSeq **SketchLen: 52788 Seqs: 738 Bases: 82339741**
In every case it used all 738 sequences and 82Mbp, and made one sketch, though the sketch size was different in the two cases since the RefSeq server uses larger-tha ...
written 5 months ago by
Brian Bushnell ♦ 17k
• updated
5 months ago by
genomax ♦ 76k
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... BBSketch servers are hosted on NERSC, which is down for ~5 days starting at 8am PST this morning for electrical work. Unfortunately, that means that they are also down. In fact, everything at JGI is down until Monday or Tuesday night. ...
written 5 months ago by
Brian Bushnell ♦ 17k
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... If it has super-low identity to anything in RefSeq, Sketch will not be able to identify it correctly. In this case the nucleotide hits are totally random; they only shared 3 sketch kmers, with estimated ANI under 76%, and Sketch is *not* accurate at under 76% ANI.
The protein results are much more ...
written 6 months ago by
Brian Bushnell ♦ 17k
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... I develop and test BBTools under Oracle JDK. For most programs, there's no significant difference between Oracle and OpenJDK. However, in some programs that use nearly all available memory, the conditions for memory crashes are different, as the two JVMs manage memory differently. For example, I ...
written 2.1 years ago by
Brian Bushnell ♦ 17k
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... Hi Andrew,
Yes, a log file would be essential here so I can see what phase it's stopping at. Additionally, the entire command line, and contents of readnamefile and refnamefile (if you used those), would be helpful, as would the BBMap version.
To clarify, are these transcriptomes of three differe ...
written 2.2 years ago by
Brian Bushnell ♦ 17k
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For A: How to download human whole genome database?
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For C: Trimming adapter sequences - is it necessary?
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For A: How do I access genome coverage using SPADES?
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For A: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files
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For A: Filter Bacterial sequences from Metagenomics
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For A: exome sequencing, target capture
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For A: Filter Bacterial sequences from Metagenomics
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