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Just curious about this. Vicuna is a virus genome aware assembler, while Trinity - as described by its developers - is an RNA assembler. What is the rationale of this choice?
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Could you clarify if Megahit is usable also for mammalian de novo assembly?
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Hello,
I will be using spades to assemble reads de-novo. I have aligned my set of reads to a genome and then I have extracted those reads which failed to align. I have decided to assemble those rea…
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Hi!
I hope this is not due to my file but when testing `vt sort` on a toy example with `-m full` (default option), I didn't get what is expected. If I try the tool `vcf-sort` on the same file, the …
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In many assemblies we are finding that assembly graph contiguity is not much higher than that of contigs extracted from it. This is true not just for miniasm but also other assemblers.
Why might th…
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Hello,
I could successfully run canu with low coverage (~10X) pacbio data.
I wonder what quality scores I can use in order to evaluate my assembly.
For example, how can I calculate N50 and how should …
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Hi,
I tried the analysis as in https://github.com/chapmanb/bcbio-nextgen/issues/2162 with also transcript_assembler activated.
I used this yaml file
```
# Template for RNA-seq using Illu…
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Hello. I'm attempting to run a hybrid assembly with test input on a HTC cluster, I've ran SPAdes v3.11.1 a few times already on this cluster without nanopore and two sets of trusted contigs, so perhap…
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Dear All,
I would like to carry out two assembly test with Canu using both the parameters sets for:
- "Smash haplotypes together"
corOutCoverage=200 ovlErrorRate=0.15 obtErrorRate=0.15
- "Av…
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Hi,
Would like to say firstly that I've been trying basically every assembler I can find for my genome, and so far SMARTdenovo has given one of the best assemblies from initial statistics, so I'm v…