User: rhall

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rhall160
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3 years, 11 months ago
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6 years, 4 months ago
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r****@pacificbiosciences.com

Posts by rhall

<prev • 16 results • page 2 of 2 • next >
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Answer: A: Tool for PacBio Denovo assembly of diploid plant genome (size 500mb) having aro
... Falcon is probably the best option, rather then try other assemblers I would try to diagnose what went wrong with the Falcon run, it's likely just a parameter problem. What is the output of DBstats ./1-preads_ovl/preads.db   With 52x of PacBio data, hybrid assembly with something like DBG2OLC wou ...
written 5.3 years ago by rhall160
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Answer: A: Install HGAP for de novo PacBio Assembly
... How large is the genome you intend assembling? For small genomes HGAP in smrtanalysis offers an end to end solution, and is the easiest way to get a 'quiver' polished assembly. HGAP isn't a single executable, it is a pipeline and make use of a large portion of smrtanalysis, it is therefore not possi ...
written 5.4 years ago by rhall160 • updated 14 months ago by _r_am32k
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Answer: A: PacBio data assembly with Celera
... fastq extracted from bax.h5 are not corrected, I would suggest using either HGAP - that is part of PacBio's SMRT Analysis system, or PBcR. http://www.pacb.com/devnet/ https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/De-Novo-Assembly http://wgs-assembler.sourceforge.net/wiki/inde ...
written 5.6 years ago by rhall160
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Answer: A: check if one unitig is truly circual
... For an up to date Celera to Gephi script: https://github.com/PacificBiosciences/Bioinformatics-Training/blob/master/scripts/CeleraToGephi.py General circularization and trimming: https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming Video how to: http://f ...
written 5.8 years ago by rhall160
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Answer: A: aligner for CORRECTED pacbio long reads
... I would suggest using Blasr, even with default parameters the alignment of corrected reads should be high quality, and parameters could be altered to more optimally map low error long reads, although I'm not sure you would gain anything other than performance (speed). Another option would be blast, ...
written 6.0 years ago by rhall160
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Answer: A: How PacBio quality is calculated?
... In a polymerase (raw) read each base has a set of QVs based on the probability of that base being incorrectly called when calculating base calls from pulses. These QVs include probability of substitution, deletion, insertion and pulse merging. The polymerase read quality is calculated as an estimati ...
written 6.3 years ago by rhall160

Latest awards to rhall

Scholar 4.2 years ago, created an answer that has been accepted. For A: How PacBio quality is calculated?
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: PacBio data assembly with Celera
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: PacBio data assembly with Celera
Scholar 5.7 years ago, created an answer that has been accepted. For A: How PacBio quality is calculated?
Scholar 6.3 years ago, created an answer that has been accepted. For A: How PacBio quality is calculated?

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