User: vijinim

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vijinim100
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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 16 months ago by vijinim100
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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 18 months ago by vijinim100
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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 19 months ago by vijinim100
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Comment: C: Binning Tools for Long Reads/Contigs
... Thank you very much. I will try it and see. :) ...
written 19 months ago by vijinim100
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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 19 months ago by vijinim100
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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 19 months ago by vijinim100
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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 19 months ago by vijinim100
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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 19 months ago by vijinim100
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Comment: C: Where can I find publicly available metagenomics contig datsets?
... Thank you very much. This is very helpful. :) ...
written 19 months ago by vijinim100
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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 20 months ago by vijinim100

Latest awards to vijinim

Popular Question 13 months ago, created a question with more than 1,000 views. For Binning of reads vs. binning of contigs in metagenomics
Popular Question 16 months ago, created a question with more than 1,000 views. For Binning of reads vs. binning of contigs in metagenomics
Student 20 months ago, asked a question with at least 3 up-votes. For What is differential abundance analysis?
Student 20 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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