Hi community.
I have a question. Did or does anyone of you ever use mothur to process their 454 sequence reads and then assemble them? The way I see it, mothur is good and quite powerful now, includes the common sequence check and pyronoise, which is helpful for correcting some homopolymer in 454. Which in my opionion is a huge problem in my work. Then naturally I came to the idea that why not first mothur then assembly?
The problem is, assembler like mira or newbler needs more than a fasta file to guarantee reasonable assembly quality. Mothur on the other hand, processes the raw sff data and when it is done, only a fasta file is generated and good to use.
So I would like to know, anyone of you has previously tried to couple mothur and say, mira? Or anyone of you has first denoised the raw sff and then assemble?
Thanks.
I have a question. Did or does anyone of you ever use mothur to process their 454 sequence reads and then assemble them? The way I see it, mothur is good and quite powerful now, includes the common sequence check and pyronoise, which is helpful for correcting some homopolymer in 454. Which in my opionion is a huge problem in my work. Then naturally I came to the idea that why not first mothur then assembly?
The problem is, assembler like mira or newbler needs more than a fasta file to guarantee reasonable assembly quality. Mothur on the other hand, processes the raw sff data and when it is done, only a fasta file is generated and good to use.
So I would like to know, anyone of you has previously tried to couple mothur and say, mira? Or anyone of you has first denoised the raw sff and then assemble?
Thanks.
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