Timeline for Separation of mixed plasmid DNA sequences post whole-plasmid sequencing
Current License: CC BY-SA 4.0
7 events
| when toggle format | what | by | license | comment | |
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| Feb 24, 2019 at 9:13 | comment | added | Jay Moore | If it's from an environmental sample might be better to try a metagenome assembler, maybe metaspades. Alternatively, use kmer spectrum to try to pull the dataset apart based on abundance, and run the assembler on cleaned-up subsets of the reads | |
| Feb 22, 2019 at 18:37 | comment | added | Roelof Coertze | Coincidentally, the DNA sample is "contaminated" genomic DNA since it was extracted from an environmental sample. That should provide the necessary SPADES training? | |
| Feb 22, 2019 at 17:06 | comment | added | Jay Moore | It looks as though plasmidSPADES expects to find some 'long' chromosomes in the mix, so it might be important to throw in some whole genome DNA into your mix of plasmids, to train the assembler. You could do this after the experiment, by appending a fastq file of E.coli genomic DNA to your fastq file of plasmid sequences... | |
| Feb 22, 2019 at 16:53 | vote | accept | Roelof Coertze | ||
| Feb 22, 2019 at 16:50 | comment | added | Roelof Coertze | Yes I had the same ideas. I am very acquainted with SPADES,although never tried de novo assembly on a mixture of plasmids. | |
| Feb 22, 2019 at 14:57 | history | edited | Jay Moore | CC BY-SA 4.0 |
added 94 characters in body
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| Feb 22, 2019 at 14:36 | history | answered | Jay Moore | CC BY-SA 4.0 |