User: fhsantanna

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fhsantanna490
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Brazil
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2 weeks, 4 days ago
Joined:
6 years, 8 months ago
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Posts by fhsantanna

<prev • 154 results • page 1 of 16 • next >
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Answer: A: Trimming reads using ivar - assembly of sars-cov-2 genome
... I found the problem. I was actually comparing results of different versions of ivar, 1.1 and 1.3. The last version was introducing more N's in the consensus, because it demands a depth of 10x for calling a base. ...
written 28 days ago by fhsantanna490
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Comment: C: Trimming reads using ivar - assembly of sars-cov-2 genome
... This was actually a good idea. I identified a region that was different between the assembly approaches. This region presents a depth mode of 3X, it was included in the original protocol, but removed when I utilized the -e option of ivar. Interestingly, the first two bases of this region presents a ...
written 28 days ago by fhsantanna490
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Comment: C: Trimming reads using ivar - assembly of sars-cov-2 genome
... Yes, if I utilize the -e option reads that don't have primers are kept. Since amplicons are fragmented during QIASeq procedure, some DNAs of the library pool probably will not have primer sites. Reads without primers are removed by default by ivar. The only program that could influence the procedure ...
written 29 days ago by fhsantanna490
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Trimming reads using ivar - assembly of sars-cov-2 genome
... I am following the workflow of Erin Young ([https://github.com/CDCgov/SARS-CoV-2_Sequencing/tree/master/protocols/BFX-UT_ARTIC_Illumina][1]) for assembly of the genomes of SARS-Cov-2. For sequencing the genomes, we utilized the QIAseq Library kit, which is based on ARTIC workflow, and the Illumina p ...
trimming ivar sars-cov-2 written 4 weeks ago by fhsantanna490
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Comment: C: Protocol for genome assembly of Sars-cov-2 sequences
... Spades is for de novo assembly, isn't it? Wouldn't a reference based assembly method be faster? ...
written 6 months ago by fhsantanna490
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Comment: C: Protocol for genome assembly of Sars-cov-2 sequences
... Yes, Kevin. It is the ampliseq panel for SARS-CoV-2. Could you please give me more details about it? I have inquired the technical support the same question, but they responded that we would have to use basespace. ...
written 6 months ago by fhsantanna490
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Protocol for genome assembly of Sars-cov-2 sequences
... Do you have a protocol using open source software for assembling SARS-CoV-2 genome sequences after Ampliseq sequencing? ...
sars genome sars-cov-2 assembly written 6 months ago by fhsantanna490 • updated 6 months ago by GenoMax94k
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Color genes/proteins based on taxonomic best-hit (bacterial genome)
... I am working with a genome sequence of a bacterial thermophile. Its genome seems to be very "chimeric", because the best-hits of each gene are from different taxonomic groups. Do you know a program to plot the genome and color its genes based on taxonomy? Something like this picture: ![https://www.n ...
hgt genome bacteria thermophiles plot written 8 months ago by fhsantanna490
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What is the difference between binning and phylotyping?
... Searching in the literature I find these terms as synonyms, but also as different processes. After all, are these terms equivalent? ...
binning metagenomics phylotyping written 17 months ago by fhsantanna490
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Comment: C: Are phylogenetic reconstruction methods considered machine-learning approaches?
... Thank you very much. As I thought, it seems only a nomenclature divergence for the same thing. ...
written 18 months ago by fhsantanna490

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