6

You might want to look into Unicycler (manuscript with more information can be found here); even though it is supposed to be used with bacterial genomes only, it might work well with a small genome such as a mitochondrion's. Beware that if you happen to have very long reads, you might end up with an assembly with multiple copies of the circular genome: you ...


5

Have you tried Mauve alignment? Its pretty easy once you become familiar and has a GUI for further ease of use. Additionally there are a few online tutorials on how to re-order contigs/ scaffolds using this software. Heres one I use when in need. Mauve contains a function called Mauve Contig Mover (MCM) which can be used to a) compare an assembly to a ...


4

There is a link to compiled binaries for OSX on the project homepage


3

I don't think you can use the --quantMode GeneCounts option with no annotations. I think the error is trying to look for an exon file generated from the annotations to do the quantitation on. Remove that and I think it should work, as the manual specifically states that annotations are optional but highly recommended.


2

I've been using ATAC to successfully align different versions of the rice genome assembly. There is a chance it will work for you between two closely related species (potato and tomato work well for example). It's not massively user friendly, but it's very fast, and it produces long, 'clean' alignments (i.e. almost all 1 to 1 alignments). The output format ...


2

Try LR_Gapcloser. I've used L_RNA_Scaffolder for trying to scaffold a genome (which turned out to be more complex than I had expected). It looks like LR_Gapcloser (written by the same people) is similar, but designed specifically for scaffolding using long-reads. That page also suggests PBJelly and GMCloser as competing tools.


2

The number of contigs and total assembly size you have suggest that there was probably more in the sequencing run than a single virus strain. Does the total assembly length correspond to expected genome size of the reference strain? Have you tried just to blast some your contigs? Could you have a contamination or something? Maybe you can just sort out the ...


1

Update 2: It looks like your approach has actually been suggested here as one way to use the PE information. I guess megahit may not be really using the PE information anyways. I still believe that it's kind of weird but other people do suggest it, so maybe it's worth trying what Torsten suggests. I think that scaffolding with PE information from the reads ...


1

I found that Viral NGS Pipeline from broad institute can actually do this. There is a python script called order_and_orient which serves this purpose. Here is the link viral ngs assembly


1

What you mean is assembly based scaffolding, as opposed to using reads with long distance information such as mate pair/long jumping distance to scaffold. You could reduce your contig file to just the longest contigs, since they have the most information. Probably 156MB of data is overkill for your virus. There are other programs out there. https://...


1

Something else that could be happening is that contigs that are being collapsed into "heterozygous" groups. This would be a particular problem when a genome has a substantial amount of repeated sequence. Digging deep into the supplementary information of the SOAPdenovo2 paper, I've found the following information: In SOAPdenovo2, heterozygous contig pairs ...


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