User: stacy734
stacy734 • 40
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Posts by stacy734
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... I have Spades running on a compute farm with 500G RAM. It is still running and only using 310G of the RAM allowed.
There is plenty of disk space (~4 TB).
I'll just let it roll.
Thanks for your comments! ...
written 6 days ago by
stacy734 • 40
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... Hi all,
I am running a genome assembly using Spades on a 1GB genome using ~120GB paired-end Illumina reads.
The process has been running for more than a week, mostly on the K-mer counting step. The log shows a notation : "Collecting K-mer information, this takes a while" so maybe this is expecte ...
written 8 days ago by
stacy734 • 40
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... Hi all,
Does anyone know if the SPAdes assembler loses singlets (unassembled strings)? In other words, if it is run on partially assembled deduped genome, will it lose all contigs that can't be further joined?
Thanks for any advice. ...
written 11 weeks ago by
stacy734 • 40
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... Hi everyone,
I recently submitted an insect genome to Genbank, and received back a very helpful report showing some contigs had contaminating bacteria. Most of this was removed prior to submission by Blasting against the bacterial db, but it looks like some were missed.
Does anyone know how to ge ...
written 4 months ago by
stacy734 • 40
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Comment:
C: Oxford Nanopore error rate?
... Thank you WouterDeCoster for posting this image.
Can you post the title of the paper? I'd like to read it for more details. ...
written 5 months ago by
stacy734 • 40
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C: Oxford Nanopore error rate?
... No, sadly there is no reference genome available. This would be for de novo assembly. ...
written 5 months ago by
stacy734 • 40
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... I'm considering trying the Oxford Nanopore sequencer.
I know at one point they had a very high error rate, which they advertise as being much lower now. I'm looking for a recent paper from an unbiased source that has tested what the error rate is in a real world process.
I have emailed the compa ...
written 5 months ago by
stacy734 • 40
• updated
5 months ago by
WouterDeCoster ♦ 42k
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Answer:
A: Advice on Blast output
... Thanks!
For others who may read this, the parameter in question can either be sskingdom or sblastname.
Stacy ...
written 9 months ago by
stacy734 • 40
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... Hi everyone,
I am running blastn on the commandline, trying different options for formatting. This command:
blastn -query blastme.fasta -out remote.blastn -db nr -evalue 1e-30 -outfmt 18 -max_target_seqs=1 &
Gives output that looks like this:
_________________________________
Accession ...
written 9 months ago by
stacy734 • 40
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... Thanks finswimmer.
Sadly, that didn't seem to solve the problem. ...
written 11 months ago by
stacy734 • 40
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