Moderator: Brian Bushnell

gravatar for Brian Bushnell
Reputation:
16,440
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Location:
Walnut Creek, USA
Website:
http://sourceforge.net...
Last seen:
2 months, 1 week ago
Joined:
4 years, 11 months ago
Email:
b********@lbl.gov

I like to program in Java.

Posts by Brian Bushnell

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Comment: C: BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
... 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 12 weeks ago by Brian Bushnell16k
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Comment: C: BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
... 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 12 weeks ago by Brian Bushnell16k
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Answer: C: BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
... 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 12 weeks ago by Brian Bushnell16k • updated 12 weeks ago by genomax73k
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Comment: C: BBSketch - A Tool for Rapid Sequence Comparison
... 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 12 weeks ago by Brian Bushnell16k
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Comment: C: BBSketch - A Tool for Rapid Sequence Comparison
... 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 3 months ago by Brian Bushnell16k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... 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 22 months ago by Brian Bushnell16k
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Comment: C: Introducing CrossBlock, a BBTool for removing cross-contamination
... 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 23 months ago by Brian Bushnell16k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... Oh, hmm, that's odd. I guess I did not read the question carefully enough. Let me edit that post... ...
written 24 months ago by Brian Bushnell16k
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Comment: C: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
... > It's smaller because the sorted reads compress more efficiently than > unsorted reads, since reads sharing sequence are adjacent in the file. > The number of reads is the same. If you decompress the files they > will be the same size. Edit - for some reason I overlooked the fact that ...
written 24 months ago by Brian Bushnell16k
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Comment: C: Calling SNPs with low coverage
... Oh, that version is too old. CallVariants was not added until v36.55 (but I recommend the latest, 37.61). ...
written 24 months ago by Brian Bushnell16k

Latest awards to Brian Bushnell

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: exome sequencing, target capture
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Scholar 7 months ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Appreciated 7 months ago, created a post with more than 5 votes. For A: Filter Bacterial sequences from Metagenomics
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Rename Duplicate ID's for Different Fasta Sequences on Windows 7
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: [samopen] SAM header is present: xxx sequences.
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: exome sequencing, target capture
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to calculate genome side????
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Pre-processing And Quality Control of the Raw NGS Data -- > trimming
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: CUTADAPT in windows
Commentator 15 months ago, created a comment with at least 3 up-votes. For A: Phylogenetic trees from nucleotide sequence, nucleotide sequences of the entire
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Benchmark - Comparison of Different NGS Mappers
Scholar 15 months ago, created an answer that has been accepted. For A: why we still need PCR before NGS even when there are brige amplifications for si
Scholar 15 months ago, created an answer that has been accepted. For A: exome sequencing, target capture
Scholar 15 months ago, created an answer that has been accepted. For A: How to download human whole genome database?
Scholar 15 months ago, created an answer that has been accepted. For A: all-mapper for differently trimmed mates
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How to identify 16s sequences from binning data(contigs)?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Extending ends of sequences with the help of reads?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Duplicates on Illumina
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Why 50bp Illumina run produces 51bp long sequencs?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How To Extract A Subset Of Reads In Fastq Using An Id List?

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