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Forum: Bioinformatics 05-13-2014, 06:30 AM
Replies: 2
Views: 1,893
Posted By krobison
KHMER (http://khmer.readthedocs.org/en/v1.0.1/)...

KHMER (http://khmer.readthedocs.org/en/v1.0.1/) may be of interest to you as it is designed for filtering & binning large read sets such as would result from a metagenomic sample
Forum: Bioinformatics 03-24-2014, 06:11 AM
Replies: 5
Views: 1,844
Posted By krobison
#!/usr/bin/perl #!/usr/bin/perl # debugging...

#!/usr/bin/perl
#!/usr/bin/perl
# debugging left as exercise for student :-)
use strict;

foreach my $arg(@ARGV)
{
my %lengths=();
# read sequence file for lengths
my $rdr=new...
Forum: General 02-28-2014, 05:20 PM
Replies: 10
Views: 1,923
Posted By krobison
Oxford is probably a poor choice for sequencing...

Oxford is probably a poor choice for sequencing targeted regions, given that most targeted sequencing is looking for small variations (such as SNPs) and Oxford looks out-of-the-box to not be well...
Forum: Metagenomics 02-20-2014, 09:06 PM
Replies: 6
Views: 3,294
Posted By krobison
If you are mostly doing targeted 16S sequencing,...

If you are mostly doing targeted 16S sequencing, then the PacBio RS II is generating interesting data in Circular Consensus mode. Clearly not everyone is going to buy one, but equally clearly you...
Forum: Sample Prep / Library Generation 02-20-2014, 09:01 PM
Replies: 8
Views: 1,567
Posted By krobison
What are you sequencing? You might be better off...

What are you sequencing? You might be better off using long reads (PacBio or Moleculo), which won't be 40Kb but given the recent successes (such as assembling an entire Drosophila chromosome arm)
...
Forum: Events / Conferences 02-10-2014, 06:42 AM
Replies: 4
Views: 1,321
Posted By krobison
I will be there; free drinks are not hard to find...

I will be there; free drinks are not hard to find in the evenings!
Forum: Pacific Biosciences 02-05-2014, 04:58 AM
Replies: 7
Views: 3,362
Posted By krobison
You may also want to look into optical mapping &...

You may also want to look into optical mapping & related -- Nabsys has not yet launched their system, but OpGen and BioNano Genomics do have optical mapping solutions that you can access as a service...
Forum: Bioinformatics 12-14-2013, 11:32 AM
Replies: 2
Views: 1,756
Posted By krobison
ClustalO is designed only for proteins; it really...

ClustalO is designed only for proteins; it really isn't an appropriate tool for transcriptomes unless you have found the ORFs and translated them.

Each file you give ClustalO would be one set of...
Forum: Bioinformatics 11-22-2013, 07:09 AM
Replies: 5
Views: 1,512
Posted By krobison
BLAST 1.x!!! I assume you are trying to...

BLAST 1.x!!!

I assume you are trying to align a lot of sequences; otherwise it is probably about a page of code in any modern programming language & a good exercise for a beginning student.
Forum: Pacific Biosciences 11-20-2013, 06:19 AM
Replies: 9
Views: 3,581
Posted By krobison
Another hybrid assembler worth noting is Cerulean...

Another hybrid assembler worth noting is Cerulean

http://sourceforge.net/projects/ceruleanassembler/

and PBJelly is another PacBio scaffolder

http://sourceforge.net/p/pb-jelly/wiki/Home/
Forum: Pacific Biosciences 11-19-2013, 12:46 PM
Replies: 9
Views: 3,581
Posted By krobison
Hybrid in sense that assembly is driven by two...

Hybrid in sense that assembly is driven by two technologies.

There are all sorts of variants of hybrids -- cleaning reads (as you've described), co-assembly, merging independent assemblies made...
Forum: Bioinformatics 11-05-2013, 06:36 AM
Replies: 2
Views: 1,070
Posted By krobison
What have you done to QC your sequences? Are you...

What have you done to QC your sequences? Are you trimming them? If you map your reads back to the assembly, what insert size to you get? What range of k are you trying?

Nextera can generate very...
Forum: General 10-22-2013, 08:38 PM
Replies: 4
Views: 3,414
Posted By krobison
How much experience do you have in the sequencing...

How much experience do you have in the sequencing field? I'm not convinced any of these systems are ready for a typical physician's office, either on the laboratory side or the informatics side.
Forum: Pacific Biosciences 10-22-2013, 08:54 AM
Replies: 7
Views: 3,672
Posted By krobison
The program reads the all_norm.fa file which...

The program reads the all_norm.fa file which contains all the reads without length filtering (at least if you are using HBAR_WF.py) -- it defaults to that name but otherwise takes an argument.
...
Forum: Bioinformatics 10-22-2013, 08:31 AM
Replies: 10
Views: 1,954
Posted By krobison
Sounds like a dare! It's really a trivial...

Sounds like a dare! It's really a trivial program & good template for writing other programs that transform sequence data. A good exercise is to use Getopt::Long to set the cutoff size and overlap...
Forum: Bioinformatics 10-18-2013, 06:48 PM
Replies: 24
Views: 8,385
Posted By krobison
Minia is not the only low-memory genome...

Minia is not the only low-memory genome assembler. See this comparison
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075505
Forum: Pacific Biosciences 10-16-2013, 10:10 AM
Replies: 7
Views: 3,672
Posted By krobison
I'm not sure how to get this within the SMRT...

I'm not sure how to get this within the SMRT Portal environment, but there is a utility called length_Info.py which can be applied to your reads to get an idea of a good length cutoff. This is...
Forum: 454 Pyrosequencing 10-01-2013, 10:23 AM
Replies: 6
Views: 4,081
Posted By krobison
Knowing the genome size within an order of...

Knowing the genome size within an order of magnitude is essential. Also, why use 454? You will pay a much higher price per read than with other technologies. Perhaps for a long amplicon it will be...
Forum: Introductions 10-01-2013, 07:09 AM
Replies: 5
Views: 1,748
Posted By krobison
The Short Read Archive at NCBI and the European...

The Short Read Archive at NCBI and the European Nucleotide Archive are two sources of raw datasets. Each equipment manufacturer tends to have datasets on their technical support websites (or in...
Forum: Ion Torrent 09-27-2013, 05:56 AM
Replies: 121
Views: 100,774
Posted By krobison
Huh??? That's backwards from my experience; did...

Huh??? That's backwards from my experience; did you mean "Ion" where you wrote "Illumina"?
Forum: Metagenomics 09-27-2013, 05:53 AM
Replies: 1
Views: 1,388
Posted By krobison
see previous thread...

see previous thread http://seqanswers.com/forums/showthread.php?t=14372
Forum: Complete Genomics 09-18-2013, 06:02 AM
Replies: 9
Views: 9,710
Posted By krobison
Apologies; as someone whose first & last name are...

Apologies; as someone whose first & last name are often butchered, I'm usually more careful about this.
Forum: Complete Genomics 09-17-2013, 06:02 AM
Replies: 9
Views: 9,710
Posted By krobison
There are a number of programs which have been...

There are a number of programs which have been published which assess assemblies given the read data; trying them out is on my to-do list so I can't make a specific recommendation

ALE: Assembly...
Forum: The Pipeline 09-13-2013, 06:06 AM
Replies: 2
Views: 6,944
Posted By krobison
Clive Brown spoke at a recent meeting & you can...

Clive Brown spoke at a recent meeting & you can find things on Twitter; no schedule for commercialization, apparently no data shown.
Forum: Bioinformatics 09-13-2013, 06:04 AM
Replies: 5
Views: 3,614
Posted By krobison
You show a pretty mongo Perl one-liner but...

You show a pretty mongo Perl one-liner but "aren't good at scripting"? Perhaps you are selling yourself short.
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