User: Optimist

gravatar for Optimist
Optimist50
Reputation:
50
Status:
New User
Location:
India
Last seen:
4 days, 3 hours ago
Joined:
2 years, 1 month ago
Email:
c************@gmail.com

I am a highly-motivated researcher currently working in bacterial genomics and exploring wider in genomics and antibiotic resistance.
My areas of specialization include medical microbiology, host-pathogen interactions, epidemiology and biostatistics with a focus on comparative genomics of multi-drug resistant bacterial pathogens.
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.
My scientific pursuit is led by the principles of Empiricism, rationalism and scepticism.

Posts by Optimist

<prev • 32 results • page 1 of 4 • next >
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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 4 weeks ago by Optimist50
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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 5 weeks ago by Optimist50
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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 5 weeks ago by Optimist50 • updated 5 weeks ago by 5heikki8.3k
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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 5 weeks ago by Optimist50 • updated 5 weeks ago by h.mon24k
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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 7 months ago by Optimist50
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Comment: C: How to generate Protein Table file ( .ptt ) and RNA table file ( .rnt ) from a
... Hello Sej Modha, Thanks for the links you've provided. I'll read-up the protocols. I'm working on bacterial genome *Pseudomonas aeruginosa* PAO1. details regarding the assembly is added below for your perusal. RefSeq - NC_002516.2 INSDC - AE004091.2 Size (Mb) - 6.26 GC% - 66.6 Thanks & Re ...
written 7 months ago by Optimist50
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How to generate Protein Table file ( .ptt ) and RNA table file ( .rnt ) from a nucleotide fasta file?
... Hello Biostar community I need your help and inputs in generating Protein Table file ( .ptt ) and RNA table file ( .rnt ) from an assembled bacterial genome. I have Fasta & genbank files of the same. Are there any tools that can generate .ptt & .rnt files using my .fna file as input. Any ...
fasta assembly ngs ptt rnt written 7 months ago by Optimist50
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Comment: C: pipelines for pan-genome analysis
... Hello Anbrinaakbar, INPUT_all.faa is generated by BPGA upon successful execution of Option 1. INPUT PREPARATION FOR CLUSTERING. This clusters all the genome sequences under study for all the downstream analysis. You may have to re run the program using option 1. regards Optimist ...
written 9 months ago by Optimist50
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(Closed) Books on Microbial Genomics
... Hello All, Greetings Can someone please suggest books one must read to have a details understanding about bacterial genomics. Thanks a lot Regards Optimist ...
bacterial genomics written 14 months ago by Optimist50
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Pictorial representation of gene cassettes
... Hello All, A warm Christmas & New Year greetings!!! I have the gene annotations of Prophage regions in my study bacterial genome. I need help with the tools that can be used to represent my annotations pictorially. (for example I'm looking at a similar output ![prophage region][1] Thanks a l ...
genomes data representation gene cassettes written 15 months ago by Optimist50

Latest awards to Optimist

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 5 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Popular Question 17 months ago, created a question with more than 1,000 views. For Any 'Biostars' like forum exclusively for bacterial Genomics ?
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.

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