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Thank you for your answer
I allready try canu but for somme resons it dosn't get installed...
I will try to have a look at flye
But for SMRT link I don't understand to what the bas and bax files correspond to (see image)
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If you are planning to use SMRTlink then use the bax and bas files.
There are other options like flye (https://github.com/fenderglass/Flye ) and canu (https://github.com/marbl/canu) that may be better than SMRTlink and they can use the fastq files.Leave a comment:
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Which PacBio ouputs use to do novo assembly?
Hello, I was given all the outputs of the result of a whole genome sequencing of a bacteria, and there is a lot of them and I don’t understand which one of these I should use to do a novo assembly:
- 3 *.subreads.fastq
- 3 *.subreads.fasta
- 3 *.bax.h5
- 1 *.bas.h5
- 1 *.mcd.h5
- 1 *.metadata.xml
I was thinking using SMRT link to do the analysis , but I don’t know which one of these I should use.
Thanks in advance.
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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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