All Questions
7
questions
1
vote
1
answer
40
views
Hybrid assembly versus polishing for hifi and illumina reads
I will have to carry out a project of assembly using hifi reads for which I have already illumina reads and I am wondering which of the hybrid assembly or polishing would be the best option for this ...
- 23
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
470
views
Understand this Kmer plot from Merqury?
The attached figure is generated based on Illumina reads from multiple individuals compared to genome assembly. Looks like there are a lot of kmers are reads only (grey colored). Also, a blue peak (2x ...
0
votes
1
answer
591
views
How to de novo hybrid assemble with Pacbio CCS and Illumina PE reads
I would like to perform de novo genome assembly on a diploid microalgal strain.
I have two datasets:
PacBio CCS/HiFi reads, low coverage.
Illumina PE 2x150 (standard shotgun)
Does anybody have any ...
- 31
1
vote
1
answer
73
views
How many reads do I need for hybrid assembly
I have Illumina and PacBio reads and I would like to use dbg2olc for hybrid assembly.
Part of dbg2olc is SelectLongestReads which select reads that sum to ...
- 453
5
votes
1
answer
158
views
Viral Metagenomics
I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray (reference below) for de novo viral genome assembly before but I haven't done metagenomics analysis before.
...
- 719
3
votes
1
answer
141
views
Scaffolding a genome with hybrid data
I am assembling a ~500MB genome, and have ~150x long reads and ~200x 150bp PE short reads, with a ~400bp insert size.
I've done a lot of work with minimap+miniasm, and have what I think is a good set ...
- 972