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4 votes
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Velvet Optimizer automatically changes to hash-length 31

If a value for MAXKMERLENGTH was not set when compiling velveth, VelvetOptimizer just uses the default ...
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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 ... ...
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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/...
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3 votes
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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 ...
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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 ...

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