User: juanjo75es

gravatar for juanjo75es
juanjo75es80
Reputation:
80
Status:
Trusted
Location:
Spain
Website:
https://contignant.com/
Last seen:
1 day, 2 hours ago
Joined:
1 year, 8 months ago
Email:
j*********@gmail.com

As you have been nice enough to arrive here, here you have a 100€ discount coupon for any Contignant s-aligner license:

BIOSTARS100

Apply it when processing the payment.

Tip. If you think software for researchers and students should be free, I have news: me too! The same way that universities and research centers fund other tools, they should fund Contignant getting licenses for their students and research staff. It will likely cost them way less than if they had funded it from zero.

Posts by juanjo75es

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Short-Read Assembly No Reference Sequence
... He says he has no reference genome and your second link points to a paper comparing mapping tools that require a reference. The first link seems to be broken. ...
written 4 weeks ago by juanjo75es80
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Comment: C: Pac bio assembler
... I think [Flye][1] is a good one but I have not tested it with Pacbio data. [1]: https://github.com/fenderglass/Flye ...
written 5 weeks ago by juanjo75es80
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Comment: C: Building a phylogenetic tree based on some selected strains of bacteria sequence
... Yep, these sequences are too large to be aligned with common multiple-alignment software I just focused on the error you were getting from Megax. You can do what Mensur says or you can just select a shorter random sequence and align it. Something between 5000 and 20000 bp. You'll definitively get a ...
written 6 weeks ago by juanjo75es80
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Comment: C: Building a phylogenetic tree based on some selected strains of bacteria sequence
... Yes, you are doing something wrong. But without more details there could be many reasons. I guess it's just you are not aligning the sequences before trying to build the tree. You need to generate a multiple alignment. Megax can do it too. Also, you posted it with the wrong tags. That's not related ...
written 6 weeks ago by juanjo75es80
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Comment: C: How can I remove contaminants from an assembled genome?
... I don't agree with point 2. The contigs will not align except in particular areas. If contigs are large enough that's unlikely a problem. Only depending on what mapping algorithm you use that could be a problem. It's not with what I usually use. I can understand point 1. Not so much point 3, I thin ...
written 7 weeks ago by juanjo75es80
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Answer: A: Mapping illumina seq reads to bacterial reference genome.
... If your contigs are large enough (larger than 3000 bp), get a subsequence of a contig (maybe 10000 bp) and make a BLAST search on the NCBI portal. You will get there a list of results with links to the complete sequences. If your contigs aren't large enough, there are three options: - Your reads a ...
written 7 weeks ago by juanjo75es80
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Comment: C: How to identify lineages from whole genome assemblies
... I guess there is no standard way to do that and that's why phylogenetic trees are still a thing. If there were another way we would not use these. As you likely know, phylogenetic trees have some limitations. ...
written 7 weeks ago by juanjo75es80
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Answer: A: bacterial genome assembly output from canu
... I think Quast is a good tool for that. It already aligns the assembly to the reference independently of any issue with circularity. I think it's also useful to get two different assemblies with two different software. Sometimes it's just the assembler that fails. Here you have a likely real rearran ...
written 7 weeks ago by juanjo75es80
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Comment: C: How can I remove contaminants from an assembled genome?
... But why do you want to do that? If you are trying to get scaffolds, the contamination will just not match. If you want to map the contigs to a reference they won't match either. I'm curious about for what use of the contigs removing contaminants is a need. ...
written 7 weeks ago by juanjo75es80
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Answer: A: don't know exactly how to find my reference genome
... In general, I would recommend you making a BLAST search in the ncbi online BLAST tool. Take one of your contigs and select around 10.000 bps and make a search. Sometimes there is no standard reference genome but someone already sequenced your species. And sometimes what you are assembling is not exa ...
written 8 weeks ago by juanjo75es80

Latest awards to juanjo75es

Autobiographer 7 weeks ago, has more than 80 characters in the information field of the user's profile.
Popular Question 15 months ago, created a question with more than 1,000 views. For Multiple alignment software
Scholar 17 months ago, created an answer that has been accepted. For A: Multiple alignment software

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