All Questions
5
questions
2
votes
2
answers
233
views
Improving prokaryotic assembly with other contig/scaffold-level data?
I have what at first sight appears to be a high-quality MAG (~10 pieces, high completion%) that I built from a hybrid assembly (Illumina + Nanopore data) from a cyanobacterium.
Workflow:
Quality ...
- 1,007
0
votes
1
answer
821
views
nanopore - where to retrieve information from the basecaller used
Where can I find information about the basecaller used in a specific nanopore run (we have a Gridion machine)?
I know already that we have Guppy v. 3.0.3, which I ...
- 283
2
votes
1
answer
430
views
Is nanopolish worth it since faster polishing software is available?
For Oxford Nanopore contigs produced by any long-read assembler has anyone performed any benchmarks to compare the polishing tools racon, ...
- 3,181
7
votes
1
answer
380
views
wtdbg2: practical implications of k-mer fsize and psize choice
I am using wtdbg2 2.3 to assemble a human genome (sequenced on PromethION from a cell line). I filtered out reads with low average quality, and now I am trying to determine the parameters that will ...
- 5,090
18
votes
1
answer
652
views
How can I improve a long-read assembly with a repetitive genome?
I'm currently trying to assembly a genome from a rodent parasite, Nippostrongylus brasiliensis. This genome does have an existing reference genome, but it is highly fragmented. Here are some ...
- 14.7k