User: Optimist
Optimist • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- India
- Last seen:
- 1 week, 1 day ago
- Joined:
- 3 years, 6 months ago
- Email:
- c************@gmail.com
I am a highly-motivated researcher currently working in bacterial genomics and exploring deeper in Antimicrobial Resistance.
My areas of specialization include medical microbiology, host-pathogen interactions, epidemiology and biostatistics with a focus on comparative genomics of clinically isolated drug resistant bacterial Pseudomonas.
Backed by strong foundations in molecular and microbiology, my skill set includes PCR, Pan and Core genome analysis, phageomics, phylogenetic analysis and biostatistics.
As an extrovert and an excellent team player equipped with efficient communication and leadership skills, I would like to collaborate in diverse and multidisciplinary teams working towards achieving the common goal of making advances in human disease treatment.
Posts by Optimist
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... I have used ISFinder. ...
written 4 months ago by
Optimist • 90
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... I want to identify transposons and presence of transposase proteins in my bacterial genome, but don't know exactly which tool has good performance, any suggestion?
My genome is a complete genome with 4 mb size.
Stay indoors and Keep safe
Thanks in advance
...
written 4 months ago by
Optimist • 90
• updated
4 months ago by
lakhujanivijay ♦ 5.1k
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... Dear Micheal Dondrup,
Please see the [image][1] for reference.
Thank You
[1]: http://www.scielo.br/img/revistas/aabc/v91s1//0001-3765-aabc-201820180762-f01.jpg ...
written 6 months ago by
Optimist • 90
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... Hi Sart!!
I use the following workflow to download a large set of Bacterial genomes from NCBI. This helped me to even download 1000s of genomes.
Execute this workflow stepwise:
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt (download the complete list of ...
written 7 months ago by
Optimist • 90
• updated
7 months ago by
Istvan Albert ♦♦ 84k
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... RGI HEATMAP should help you solve this issue.
usage: rgi heatmap [-h] -i INPUT
[-cat {drug_class,resistance_mechanism,gene_family}] [-f]
[-o OUTPUT] [-clus {samples,genes,both}]
[-d {plain,fill,text}] [--debug]
Creates a heatmap when given m ...
written 7 months ago by
Optimist • 90
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... Dear Emily,
Thank You for the prompt response.
I would like to make an image with the Genetic Context of particular region of a bacterial genome. I would like to know if there is a tool that can help me generate the image. [Link to reference image][1]
[1]: http://www.scielo.br/img/revistas/aab ...
written 8 months ago by
Optimist • 90
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... Could someone help me with a tool to generate genetic context images between two or multiple genomes.
Thanks in advance ...
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... There is no Illumina data available for the isolates under study. ...
written 11 months ago by
Optimist • 90
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Comment:
C: Nanopore only assembly errors
... Hi all,
I have assembled multiple bacterial genomes sequenced using Oxford Nanopore Minion (FLO-MIN106 flowcell) sequencer.
I have used Pomoxis, Unicycler assemblers to perform the genome assembly. Upon annotating the resultant fasta files of the genome assembly using RAST and PATRIC, I have obser ...
written 11 months ago by
Optimist • 90
4
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1
answer
373
views
1
answer
... Hi all,
I have assembled multiple bacterial genomes sequenced using Oxford Nanopore Minion (FLO-MIN106 flowcell) sequencer.
I have used Pomoxis, Unicycler assemblers to perform the genome assembly. Upon annotating the resultant fasta files of the genome assembly using RAST and PATRIC, I have obser ...
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For Any 'Biostars' like forum exclusively for bacterial Genomics ?
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For Any 'Biostars' like forum exclusively for bacterial Genomics ?
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