User: vijinim

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vijinim90
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Posts by vijinim

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Binning Tools for Long Reads/Contigs
... I'm not sure. But what I'm looking for is an alignment-free binning tool, and it seems there is no such tool for long reads at the moment. ...
written 4 weeks ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... There seems to be no proper tool to do de novo (taxonomy independent) binning of long reads. All available methods are based on taxonomical binning. ...
written 3 months ago by vijinim90
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Answer: A: Binning Tools for Long Reads/Contigs
... I found a tool named [MEGAN-LR][1] which can bin metagenomic long reads and contigs. Although it is based on taxonomical binning, I'm going to try it and see. Thank you all for your insights and ideas. :) [1]: https://biologydirect.biomedcentral.com/articles/10.1186/s13062-018-0208-7 ...
written 3 months ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... Thank you very much. I will try it and see. :) ...
written 3 months ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... Yes. I think this is the issue. I will find another software to do binning. Thank you very much for your insights and explanations. :) ...
written 3 months ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... I used Escherichia coli CFT073 and Staphylococcus aureus JP080. When we get short reads and bin the contigs, MaxBin produces 2 bins with good results. Similarly, I tried MaxBin with long reads from the same 2 genomes but it gave only 1 bin. ...
written 4 months ago by vijinim90
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Comment: C: Binning Tools for Long Reads/Contigs
... I believe there is no difference apart from the effects of the error rates of short reads and long reads. However, I tried to bin a simulated dataset of reads from 2 bacterial genomes (with 20kb - 21kb read lengths and 10% error rate) and the tool failed to identify two bins. It produced only one ...
written 4 months ago by vijinim90
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Binning Tools for Long Reads/Contigs
... Majority of the currently available metagenomics binning tools are designed to work with short reads and contigs obtained from short reads. Does someone know if there are any tools available to bin long reads or contigs obtained from long reads? Thank you very much! :) ...
long reads metagenomics contigs binning written 4 months ago by vijinim90
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Comment: C: Where can I find publicly available metagenomics contig datsets?
... Thank you very much. This is very helpful. :) ...
written 4 months ago by vijinim90
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Comment: A: Where can I find publicly available metagenomics contig datsets?
... I did not find any annotated datasets up to now. What researchers have done is obtain a publicly available set of reads, assemble it using an assembly software, obtain the contigs and use the tool [TAXAassign v0.4][1] to determine the origin species of these contigs. [1]: https://github.com/umer ...
written 4 months ago by vijinim90

Latest awards to vijinim

Popular Question 26 days ago, created a question with more than 1,000 views. For Binning of reads vs. binning of contigs in metagenomics
Student 4 months ago, asked a question with at least 3 up-votes. For What is differential abundance analysis?
Student 4 months ago, asked a question with at least 3 up-votes. For Binning of reads vs. binning of contigs in metagenomics
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