User: arunprasanna83

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Posts by arunprasanna83

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Comment: C: Troubleshooting assembly contigs of large genome
... I am using mummer 3.2.3. As @gconception mentioned I will try 4. How does blastn help ? ...
written 3 months ago by arunprasanna8330
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Comment: C: Troubleshooting assembly contigs of large genome
... I used mummer 3.2.3. I will give 4 a try !. Btw. D-GENIES web version failed and a local installation is not friendly. The assemblies are from long reads and assembled with Canu. ...
written 3 months ago by arunprasanna8330
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Troubleshooting assembly contigs of large genome
... Hello, Following is my strange situation: I assembled genomes from same sample (haploid source) with two different methods. Assembly size of two methods are the following: Method1 = 900 Mb (5400 contigs >10kb) Method2 = 500 Mb (7000 contigs >10kb) I suspected duplication in Method 1 and ch ...
genome assembly alignment sequencing written 3 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... As I mentioned in comments above, AliTV is also working fine for smaller files. But for bigger files it is taking forever. I guess there is no parallelization option. ...
written 3 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... Symap worked for comparing small vs big assembly. But it is still running for other case 'big vs big' assembly (910 Mb, 5931 contigs) for self comparison over 5 days !. Any tips ? ...
written 3 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... Sure ! I am doing it in my linux workstation with 150 GB RAM and 40 Cores. ...
written 3 months ago by arunprasanna8330
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Comment: A: Visualizing contig alignment
... There is a bigger problem here. Most of these programs crash due to large file size. i.e File 1 has 44k contigs (510MB) and File 2 has 5900 contigs (910 MB). To make it easier, I tried to merged respective files into single long sequence. But still, the programs crashes ! Any solutions to handle the ...
written 3 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... Will try Circlize or AliTv. Because, I tried both Gepard & minidot. Both failed due to large file size ! ...
written 3 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... Thanks ! Out of these, symap is doing a neat job !. ...
written 3 months ago by arunprasanna8330
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Comment: C: Visualizing contig alignment
... Thanks @lieven.sterck. I did send them an email 3 weeks back. But did not get any response !. So moved on to explore other options. ...
written 3 months ago by arunprasanna8330

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