User: fhsantanna

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fhsantanna410
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Brazil
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Posts by fhsantanna

<prev • 128 results • page 1 of 13 • next >
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Software to group full length 16S rRNA sequences based on identity threshold
... 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 ...
species rrna 16s identity matrix written 11 weeks ago by fhsantanna410 • updated 10 weeks ago by Carambakaracho510
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Comment: C: Criteria for filtering contigs after spades assembly
... 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 8 months ago by fhsantanna410
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Comment: C: Criteria for filtering contigs after spades assembly
... Good idea. I'll give it a try. ...
written 8 months ago by fhsantanna410
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Comment: C: Criteria for filtering contigs after spades assembly
... 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 8 months ago by fhsantanna410
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Criteria for filtering contigs after spades assembly
... 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 ...
assembly spades contigs filtering written 8 months ago by fhsantanna410
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Answer: A: Make motif position matrix based on multiple sequence alignment.
... http://meme-suite.org/doc/jaspar2meme.html ...
written 15 months ago by fhsantanna410
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Comment: C: How to recover a 16S rRNA gene from genome reads?
... Nice suggestions. I'll give a try. Soon I post a feedback. ...
written 17 months ago by fhsantanna410
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Comment: C: Upgrade Ubuntu 16.04 to Bio Linux 8
... You mean **downgrade** to Biolinux. Biolinux is based on Ubuntu 14.04 version. I recommend not doing it. ...
written 18 months ago by fhsantanna410
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How to recover a 16S rRNA gene from genome reads?
... 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 ...
genome rrna denovo assembly written 18 months ago by fhsantanna410 • updated 7 months ago by felipe.zoujiro20
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Answer: A: How to remove contigs below 201 nuclotide from a genome assembly?
... 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 18 months ago by fhsantanna410

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Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to create a Venn diagram using ortholog clusters?
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