New answers tagged assembly
4
votes
Accepted
Velvet Optimizer automatically changes to hash-length 31
If a value for MAXKMERLENGTH was not set when compiling velveth, VelvetOptimizer just uses the default ...
- 2,156
0
votes
How to find specific types of assemblies for specific species using entrez tools?
I strongly recommend switching to SRA https://www.ncbi.nlm.nih.gov/sra
Whether the following would work ...
...
M__♦
- 9,149
2
votes
Improving prokaryotic assembly with other contig/scaffold-level data?
Summary
What I am saying in this post is there approximates to 3 "generations" of in silico gap-closers/polishes:
GapFiller - amongst other "early" generations (2012);
medaka/...
M__♦
- 9,149
3
votes
Accepted
How to subset an SRA file for a single chromosome?
After dumping out the reads using fasterq-dump, you'll need to align them first and then extract those that map to your region of interest. I think minimap2 is an ...
- 2,156
2
votes
Accepted
Improving prokaryotic assembly with other contig/scaffold-level data?
If your goal is to compare to the NCBI version I'd suggest using QUAST to compare the two assemblies, supplying the NCBI assembly as the reference genome (-r option ...
- 3,259
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