All Questions
Tagged with assembly software-recommendation
5
questions
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
2
votes
0
answers
353
views
Platanus-allee phasing fail: Error(13): Error, SolveDBG exception!
I am using Platanus-allee 2.2.2 for heterozygous genome (~500mb) assembly with Illumina short reads and PacBio reads input data.
I have the file contigs.fa from short reads but phasing step with ...
- 21
2
votes
3
answers
258
views
What assembler is appropriate for High-Fidelity PacBio reads
What assembler is appropriate for High-Fidelity PacBio reads?
For example, canu is good for high-error PacBio reads. But what algorithm to use for HiFi reads? Would it be OK to use canu without the ...
- 2,469
8
votes
2
answers
2k
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estimate genome size: kmer-based approach from PacBio reads
Can anyone suggest a software/method for kmer analysis using PacBio reads (RSII)?
Something similar to Jellyfish, that I saw in a nice tutorial - but must be suitable for long, noisy reads. ...
- 2,706
4
votes
2
answers
439
views
Reordering scaffolds according to a reference without a genetic map
I am trying to reorder scaffolds of a rice species, but no genetic map is available right now. Oryza sativa Japonica is a close relative of this rice species. Mummer was used to do a whole genome ...
- 325