We have sequenced environmental sample in triplicates resulting in 16 Gb raw data (fast5)
I would like to know the pipeline to assemble and annotate the whole genome.
Thank you in advance
Van Damme R, Hölzer M, Viehweger A, Müller B, Bongcam-Rudloff E, Brandt C (2021) Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLoS Comput Biol 17(2): e1008716. https://doi.org/10.1371/journal.pcbi.1008716
At first, you need to conduct basecalling process. Guppy is the most commonly used. If you have a GPU server, I strongely recommend Bonito, which can supply a much higher accuracy than Guppy. Next you can proceed assembly part. We supply the whole metagenomic analysis servicve based on data from differernt sequecning platforms. You can contact us for help.
Take a look at Flye using the --meta option. Flye works very well with nanopore data and handles uneven coverage. https://github.com/fenderglass/Flye
John M. Sutton
Thank you for suggesting Flye, As I used and got more than 6k sequences in a FASTA file. How do I know about the complete genome assembly of bacterial spp? Because the FASTA file containing a diverse range of bacterial sequences.
Thank you
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