Originally posted by lilou
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Interesting. HGAP4 Manual doesn't mention this, but the FALCON GitHub repo does - the impression that SMRTLink software gives is that it is a GUI wrapper for FALCON. I guess not. Thanks. -
Hello
HGAP does not support this size of genome. It is made for <=3Gb genomes.
Best to use Falcon which is also a diploid aware assemblerLeave a comment:
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Well, finally got version 8 installed. It never completes, just hangs forever. Seems like a terrible assembler.Leave a comment:
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Oh my, that's a big one. How much memory is it using?
If you just want a rough assembly, I would do wtdbg2 as you can get a sense of contig lengths without consensus generation. I've done flye with 10X read coverage (to look at how much is chloroplast and bacteria in a dirty sample) and it didn't protest. Sorry, haven't used HGAP.Leave a comment:
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Well, figured it out - was a corrupted file from the download!Originally posted by SNPsaurus View Post
Wood Frog Genome - 6 Gbp
Got it working, but it barfs as it wants to fo a 30x coverage and from the RAW reads, it comes up a few thousand short. Would the SEED COVERAGE parameter (in the Advanced tab) be the one I would want to change? From say 30 to 25? (Just to get a rough assembly?) I'm waiting on HiSeq data to do a combined ONT + Pac Bio + HiSeq assembly in CANU.Leave a comment:
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What kind of genome are you trying to assemble? I usually go with flye as a first pass (fast, memory efficient) and then Canu if flye underperforms (they seem to trade off which gives a better assembly in our hands). wtdbg2 is fun to try a quick check but I don't think it is as feature complete as flye or canu.Leave a comment:
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SMRT Link 7.0 - HGAP
Has anyone gotten the HGAP assembler to work? It seems that it just barfs at different places constantly. Doesn't seem to be very robust at all.
I've used CANU before, so I'm going to try to go back to that...
What about the wtdbg2assembler?
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My mistake - a corrupted downloaded data file was the culprit; should have checked the mdm5 checksum before starting!
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Amplicon sequencing is a targeted approach that allows researchers to investigate specific regions of the genome. This technique is routinely used in applications such as variant identification, clinical research, and infectious disease surveillance. The amplicon sequencing process begins by designing primers that flank the regions of interest. The DNA sequences are then amplified through PCR (typically multiplex PCR) to produce amplicons complementary to the targets. RNA targets...03-21-2023, 01:49 PM -
Targeted sequencing is an effective way to sequence and analyze specific genomic regions of interest. This method enables researchers to focus their efforts on their desired targets, as opposed to other methods like whole genome sequencing that involve the sequencing of total DNA. Utilizing targeted sequencing is an attractive option for many researchers because it is often faster, more cost-effective, and only generates applicable data. While there are many approaches...03-10-2023, 05:31 AM
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