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Search: Posts Made By: themerlin
Forum: Bioinformatics 11-17-2015, 05:04 PM
Replies: 2
Views: 1,219
Posted By themerlin
I know folks who use Kraken for this sort of...

I know folks who use Kraken for this sort of thing.

https://ccb.jhu.edu/software/kraken/

Jason
Forum: Bioinformatics 03-11-2015, 10:36 AM
Replies: 2
Views: 1,574
Posted By themerlin
How do you have you SNP data arranged? If it is...

How do you have you SNP data arranged? If it is a multi-FASTA, you should be able to build a tree with most tree building applications. If it's in another format, you'll likely need to get it into...
Forum: Bioinformatics 08-28-2014, 11:38 AM
Replies: 2
Views: 2,158
Posted By themerlin
No promises that it works correctly, but here's...

No promises that it works correctly, but here's something that I had sitting around:

https://gist.github.com/jasonsahl/9306cd014b63cae12154

You need BioPython to run and it assumes no gaps. In...
Forum: Bioinformatics 02-06-2014, 10:33 AM
Replies: 9
Views: 3,780
Posted By themerlin
I'd give Prokka a try: ...

I'd give Prokka a try:

http://www.vicbioinformatics.com/software.prokka.shtml
Forum: Bioinformatics 01-27-2014, 06:42 AM
Replies: 2
Views: 904
Posted By themerlin
This web server might be what you're looking for:...

This web server might be what you're looking for:

http://cge.cbs.dtu.dk/services/snpTree/
Forum: Bioinformatics 09-24-2013, 02:23 PM
Replies: 4
Views: 2,613
Posted By themerlin
If you have a SNP table of only core SNPs, they...

If you have a SNP table of only core SNPs, they should all be the same length and you shouldn't have to do any subsequent alignment; meaning that when you convert your SNP table to a multi-fasta, all...
Forum: Bioinformatics 08-10-2013, 11:52 AM
Replies: 4
Views: 1,309
Posted By themerlin
Victor, If you are doing a SNP analysis...

Victor,

If you are doing a SNP analysis against a reference, just include your reference as an external genome, as well as the reference, and it should be processed with the rest of your external...
Forum: Bioinformatics 08-06-2013, 07:39 AM
Replies: 6
Views: 2,992
Posted By themerlin
Victor, If you have an aversion to command...

Victor,

If you have an aversion to command line tools, you could try this web server:

http://cge.cbs.dtu.dk/services/snpTree/

You can upload assemblies, fastqs, vcfs, and/or bams and it will...
Forum: Bioinformatics 08-05-2013, 11:39 AM
Replies: 6
Views: 2,992
Posted By themerlin
How many genomes are you working with? And are...

How many genomes are you working with? And are you working with assemblies or raw reads?

For a smaller number of genome assemblies, you could do whole genome alignments with Mugsy...
Forum: Bioinformatics 07-15-2013, 07:48 AM
Replies: 7
Views: 2,699
Posted By themerlin
If you will have future python scripts that will...

If you will have future python scripts that will use BWA, then it would be worth the time to create a python function that calls bwa. If it is a one time thing, a shell script should be fine.
Forum: Bioinformatics 12-17-2012, 11:12 AM
Replies: 4
Views: 6,046
Posted By themerlin
Mira MAF is different than the MAF produced by...

Mira MAF is different than the MAF produced by whole genome aligners - the Mira MAF is unique to that program.
Forum: Bioinformatics 12-17-2012, 09:09 AM
Replies: 4
Views: 6,046
Posted By themerlin
The galaxy tool is built on these libraries...

The galaxy tool is built on these libraries (https://bitbucket.org/james_taylor/bx-python/wiki/Home). They also include scripts to join blocks together before converting to fasta
Forum: Bioinformatics 12-12-2012, 01:25 PM
Replies: 1
Views: 846
Posted By themerlin
If you want Robinson-Foulds values, try: ...

If you want Robinson-Foulds values, try:

hashrf (https://code.google.com/p/hashrf/)
treedist (http://evolution.genetics.washington.edu/phylip/doc/treedist.html)
phangorn...
Forum: Bioinformatics 11-29-2012, 06:56 AM
Replies: 13
Views: 2,238
Posted By themerlin
Yes, it is hard to install. When you run ARB,...

Yes, it is hard to install. When you run ARB, click on 'CREATE and IMPORT'. Find your own alignment, click 'auto detect', and select fasta_wgap, then go. There will be a list of all of the reads...
Forum: Bioinformatics 11-26-2012, 06:25 PM
Replies: 13
Views: 2,238
Posted By themerlin
The alignment editor in ARB is pretty nice. It...

The alignment editor in ARB is pretty nice. It is designed for 16S analysis, but I've also looked at whole genome alignments. You can move gaps, change bases, design primers, etc.
...
Forum: Bioinformatics 11-15-2012, 02:32 PM
Replies: 9
Views: 4,279
Posted By themerlin
I think that this will require some testing. ...

I think that this will require some testing. Start high and work down until you hit the sweet spot for your analysis.
Forum: Metagenomics 11-06-2012, 07:06 AM
Replies: 3
Views: 2,553
Posted By themerlin
I assume that when you say "metagenomic data" in...

I assume that when you say "metagenomic data" in this context, you mean you have 16S rRNA data from mixed microbial communities.

If you are interested in species, you might check out speciate-it...
Forum: Bioinformatics 10-30-2012, 03:42 PM
Replies: 9
Views: 4,279
Posted By themerlin
USEARCH might also be an option: ...

USEARCH might also be an option:

http://www.drive5.com/usearch/

After clustering at any level of ID, you can output either a consensus sequence or a centroid sequence for each cluster.
Forum: Bioinformatics 10-21-2012, 06:49 AM
Replies: 4
Views: 1,721
Posted By themerlin
Thanks for your reply. I figured that there was...

Thanks for your reply. I figured that there was a solution, but I didn't want to re-invent the wheel if someone had already written something that works. I will start writing a script following...
Forum: Bioinformatics 10-19-2012, 08:46 AM
Replies: 4
Views: 1,721
Posted By themerlin
Opgen MapSolver output to fasta scaffold?

Greetings,

I'm trying to close a genome using optimal maps and sequence data. I have mapped my contigs to the Whole Genome Map and was hoping to try and close gaps in the scaffold. I know that...
Forum: Bioinformatics 10-01-2012, 09:01 AM
Replies: 4
Views: 1,454
Posted By themerlin
Maybe brig is what you have in mind? ...

Maybe brig is what you have in mind?

http://sourceforge.net/projects/brig/
Forum: Bioinformatics 09-17-2012, 08:42 PM
Replies: 4
Views: 933
Posted By themerlin
Try either shuffleSequences_fastq.pl included...

Try either shuffleSequences_fastq.pl included with Velvet or this:

http://www.ngcrawford.com/2012/03/28/interleave-paired-end-reads/
Forum: Bioinformatics 09-04-2012, 09:02 AM
Replies: 3
Views: 2,646
Posted By themerlin
I'm not sure that you can create a tree from a...

I'm not sure that you can create a tree from a MAF file with overlapping reads. With Mugsy, you usually provide separate files for each genome and then infer a tree from sequence conserved in each...
Forum: Bioinformatics 08-29-2012, 11:37 AM
Replies: 3
Views: 2,646
Posted By themerlin
I'm a little unclear about your question. If you...

I'm a little unclear about your question. If you have contigs, then you are working with an assembly. Do you mean that you are working with overlapping paired-end reads?
Forum: Metagenomics 08-15-2012, 04:38 PM
Replies: 3
Views: 3,401
Posted By themerlin
You could try SSU-align ...

You could try SSU-align

http://selab.janelia.org/software.html

Works well on whole genome data to pull out 16S, but I don't know how slow it would be on large metagenome datasets.
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