User: Optimist

gravatar for Optimist
Optimist70
Reputation:
70
Status:
Trusted
Location:
India
Last seen:
34 minutes ago
Joined:
2 years, 7 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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Comment: C: High CDS Count in my assembled Genome using Nanopore reads (ONT) data
... There is no Illumina data available for the isolates under study. ...
written 23 days ago by Optimist70
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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 27 days ago by Optimist70
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High CDS Count in my assembled Genome using Nanopore reads (ONT) data
... 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 ...
wgs high cds nanopore assembly written 29 days ago by Optimist70 • updated 29 days ago by h.mon27k
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Download All The Bacterial Genomes of Pseudomonas aeruginosa From Ncbi
... Dear members of Biostar!! Greetings I would like to download all the genomes available with regards to Pseudomonas aeruginosa species from NCBI. Kindly let me know the way to download all the 4761 genomes for species from NCBI ([link][1]). Thanks [1]: https://www.ncbi.nlm.nih.gov/genome/?te ...
wgs ngs bacterial genomics written 3 months ago by Optimist70 • updated 3 months ago by Joe14k
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Country wise list of bacterial genome sequences
... How to get the statistics of all the available bacterial genomes that were sequenced. I need a list of bacterial genomes sequenced from India. Can anyone help me out with this issue. Thanks ...
wgs ngs bacterial genome written 3 months ago by Optimist70 • updated 3 months ago by genomax71k
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SPAdes usge commandline
... Hey guys, I'm using SPAdes (version 3.13) for assembling Ion torrent reads of Klebsiella pneumoniae. FastQC Report: Filename KP.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences: 1603362 Sequences flagged as poor quality : 0 Sequence length: 25-584 %GC : ...
genome assembly ion torrent written 6 months ago by Optimist70
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Comment: C: Is there a way to segregate Plasmid contigs from Iontorrent WGS data?
... Thank you for your answer. I need to segregate Chromosomal DNA contigs & Plasmid DNA contigs separately from a fasta file exactly like that of example ref file HS11286 you have shown. Can you please elaborate further on the solution you've given I have downloaded Klebsiella pneumoniae referen ...
written 7 months ago by Optimist70
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Is there a way to segregate Plasmid contigs from Iontorrent WGS data?
... I have a fastQ and fasta file of a klebsiella pneumoniae genome and would like to separate Plasmid contigs from WGS fasta file with 221 contigs. Separate plasmid contigs would help me characterize plasmids and resistant genes it possess using a circular representation and further enable me carry ou ...
ion torrent wgs plasmid assembly written 7 months ago by Optimist70 • updated 7 months ago by 5heikki8.5k
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Has anyone used MeDuSa: a multi-draft based scaffolder
... Hi All, Has anyone used Medusa tool to construct scaffolds from contigs? How was the experience been like? Is it 'safe' to construct scaffold in this method as it introduces 'N's in between? kindly give your inputs on these Thanks & Regards Optimist ...
wgs ngs medusa bacterial genomics written 7 months ago by Optimist70 • updated 7 months ago by h.mon27k
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Comment: C: How to generate Protein Table file ( .ptt ) and RNA table file ( .rnt ) from a
... Thank You for the quick revert. I'll follow the link you have provided. Regards Optimist ...
written 12 months ago by Optimist70

Latest awards to Optimist

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 3 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Supporter 3 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 11 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 23 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Autobiographer 2.1 years ago, has more than 80 characters in the information field of the user's profile.

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