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Apparently Illumina uses the Q=2 quality score as a "Read Segment Quality Control Indicator". I can't find any recent mentions of this on Illumina's website. One document from 2011 describes it as:
>…
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First weekly progress update of my project (description of my project plan)
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Interesting new tool from NCBI that they're applying to the SRA data!
(Text found via Analysis (alpha) tab, [linked from here](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR929453))
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Project: 2520
Position: 284-285
Looks like there should be an A inserted between those two positions
/media/VD_Research/TMPDIR/2520_Projects/A12x2520_Houston_Mesoni
@InaMBerry
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Hello
I have three questions pertaining to the VPhaser output
1) How do I interpret the output below ??
Pos Var Cons Strd_bias_pval Type Var_perc SNP_or_LP_Profile
1425…
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In preliminary testing, clumpify is much faster than mvicuna, but does not seem to remove as many reads with the settings I tried (subs=5 to match mvicuna and passes=4). On a bam file that mvicuna spe…
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Hi,
I have noticed that kmc tool (latest release) generates wrong k-mers for long (>= 32) reads and short reads (~5) as well.
For example:
AACCACAGATATCTTTAACCAGGATACCATAGAC
the following sh…
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The scaffolding stage does not always succeed for diverse genomes such as HIV or influenza.
The parameter space of the involved tools (currently `nucmer`, part of [`MUMmer`](http://mummer.sourceforge…
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Hello!
I just would like to know if technical support of Vphaser still works? If yes, where can I find it?
Sincerely,
Konstantin.
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Hi,
I'm wondering is there any way to access the taxonomic data that STAT is automatically generating on each NCBI run? Every metagenomic upload on the SRA has this analysis generated and displayed a…