User: ikangkim
ikangkim • 40
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Posts by ikangkim
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... Thank you for a comment.
(1) I didn't know that PacBio has systematic deletion at homopolymer regions.
(2) Below is the IGV snapshot image of the region where Pilon introduced 43 bp deletion. Upper is the PacBio read mapping, while the lower is the Illumina read mapping. All PacBio reads were mapp ...
written 28 days ago by
ikangkim • 40
2
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... Hi,
If genome sequences were assembled from PacBio reads and then polished with quiver/arrow iteratively, do I steel need to polish the genome sequences further with Illumina reads?
I've been trying to assemble a few dozen actinobacterial genomes. I have both PacBio and Illumina data and sequencin ...
written 4 weeks ago by
ikangkim • 40
0
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... I've been trying to optimize several parameters for guppy.
Until now, the setting below was the fastest for GPU, but the speed improvement was just ~20-25% compared to default.
$ guppy_basecaller -i /fast5 -s /guppy -c dna_r9.4.1_450bps_hac.cfg -x "cuda:0" --gpu_runners_per_device 4 --num_callers ...
written 5 weeks ago by
ikangkim • 40
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... Thank you for a reply.
I also feel that hac models would be better for downstream analyses. I think I had better spend more time to optimize guppy parameters. Currently, hac model is >10X (GPU) or >20X (CPU) slower than fast model on my machine. ...
written 5 weeks ago by
ikangkim • 40
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... Hi,
I'm planning to sequence bacterial genomes using both Nanopore and Illumina platforms to get nearly complete and accurate genomes. After getting sequence data, I'm going to perform hybrid assembly (e.g. Unicycler) or long-read assembly followed by short-read polishing.
In this case, can I get ...
written 5 weeks ago by
ikangkim • 40
3
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... https://github.com/ablab/spades/issues/40
The above page may be helpful for you. I tried with SPAdes 3.11.1 and succeeded.
In brief,
(1) To use k-mer > 127, you have to download and compile source code.
(2) Edit "spades_compile.sh" file as below and run the script.
cmake -G "Unix Makefiles" ...
written 20 months ago by
ikangkim • 40
Latest awards to ikangkim
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20 months ago,
created an answer that has been accepted.
For A: SPAdes assembler k-mer > default 127 possible?
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20 months ago,
created an answer with at least 3 up-votes.
For A: SPAdes assembler k-mer > default 127 possible?
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