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Increased mi and ml prevents the assembler 'looking for overlap' where there is not enough coverage to actually have overlap. I don't think it drops low quality reads any more than default parameters, though... -
great...
The assembly finished in 13 hours:
start: Sat Mar 27 19:21:59
stop: Sun Mar 28 08:25:07
What is the advantage of increasing the ml length or mi length with low coverage reads?
I am interested in doing additional reading on the topic and Im sure others have had the similar issues if coverage is low.
Also, I found that the N50 decreased by using large option and switching from -ml60/-mi90 parameters to default parameter (N50 = 775, N50=540).
I assume that low quality reads are dropped by setting the overlapMinMatchIdentity to a higher value, which increases contig quality. But I am unclear on this topic.Leave a comment:
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Long detangling points to a problem with the dataset. You could try the -large option which I think will solve it. It shortcuts some steps during detangling (and alignment).
If coverage is low, ie less than say 15x, also increasing alignment stringency could help: -mi 96 or 98, -ml 60, 80 or even 100.
Good luck!Leave a comment:
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454assembly using Newbler: job time expectation?
Greetings
I would like to know how long should the following assembly to run using newbler?
The following are details:
gsAssebler
software version: 2.3
Data: 454 data
Input: 3 .sff files with a total of 1,434,170 reads
Genome: eukaryotic unknown size
Not pair end.
I am using the command line and not the GUI. The manual suggests that runAssembly is faster and more efficient. In my previous jobs, I find this to be true. ie.
shell> runAssembly -g , -cpu Num 4 ./input #command used.
Hardware specs:
CPU: 4 processors 2.66ghz ea
RAM: 16gb
The 454newblerprogress.txt file shows that it is currently “detangling alignemnts”. This is great but the file has not updated for more than 24hrs!
The job is running for 6 days, a deadline is looming...
Should I assume it the newbler stalled, died or just gave up?
Thanks.
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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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