User: fhsantanna
fhsantanna • 430
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Posts by fhsantanna
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... I have a set of full length 16S rRNA sequences (~1500 nts) and I want to classify them in groups based on a identity threshold (98.5%, species circumscription threshold). What software do you recommend for this purpose?
PS1:
I tried CD-HIT, but it resulted in some awkward groupings (ie. a species s ...
written 7 months ago by
fhsantanna • 430
• updated
7 months ago by
Carambakaracho • 750
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... Interesting idea. But I believe this is not the problem. I blasted the small contigs (<1kb), and all of them matched to the expected bacterial genus.
EDIT:
In fact, I checked the contigs from other strain. I'll have to verify again if the small contigs are contamination. ...
written 13 months ago by
fhsantanna • 430
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... Good idea. I'll give it a try. ...
written 13 months ago by
fhsantanna • 430
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... Yes, it is necessary a de novo assembly, because we have sequenced a novel bacterial species. The expected length is between 5 - 6 Mpb. We have about 840,000 paired reads of ~250 bp (a raw coverage of about 80x, (2 x 250 x 840000)/5000000).
After genome assembly I have 13 contigs having more than 20 ...
written 13 months ago by
fhsantanna • 430
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... I have assembled a bacterial genome using spades.
The coverage among the contigs is very heterogeneous, while some have more than 30 fold of coverage, other have less than 5 fold. Also, there are a lot of contigs with a length less than 500 bp.
I'm aware that I must filter contigs having low coverag ...
written 13 months ago by
fhsantanna • 430
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... http://meme-suite.org/doc/jaspar2meme.html ...
written 20 months ago by
fhsantanna • 430
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... Nice suggestions. I'll give a try. Soon I post a feedback. ...
written 22 months ago by
fhsantanna • 430
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... You mean **downgrade** to Biolinux. Biolinux is based on Ubuntu 14.04 version.
I recommend not doing it. ...
written 22 months ago by
fhsantanna • 430
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... I have sequenced a bacterial genome with Illumina 2x300 pb kit and after that I have assembled the genome using SPADES (and also A5 pipeline).
The problem is that the draft genome does not present a full 1500 pb rRNA 16S gene. It is expected, since assemblers do not do a great deal with repetitive ...
written 22 months ago by
fhsantanna • 430
• updated
4 months ago by
jeremieaauger • 0
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... If you have limited bioinformatics skills, I recommend using Bioedit. With it you can sort your contigs by length, and manually exclude those not desirable.
Otherwise, you can use this fantastic toolkit: FAST (https://github.com/tlawrence3/FAST). ...
written 23 months ago by
fhsantanna • 430
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