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Forum: Bioinformatics 05-06-2018, 02:01 PM
Replies: 1
Views: 1,020
Posted By michaelbarton
Sharing benchmarking results for short read assembler on paired end Illumina data

We recently wrapped up some work on benchmarking the more recent genome assemblers on a range of genomes with Illumina paired end sequence data. We compared a few of the most common metrics, one...
Forum: Bioinformatics 03-11-2013, 12:46 PM
Replies: 2
Views: 1,327
Posted By michaelbarton
Thanks. I'm actively developing it; I just pushed...

Thanks. I'm actively developing it; I just pushed a version release in response to a request for an additional feature last week. So if you have any queries or suggestions just let me know through...
Forum: Bioinformatics 03-11-2013, 08:03 AM
Replies: 2
Views: 1,327
Posted By michaelbarton
Genomer - software to simplify genome finishing

Hi Everyone,

I wrote some software to simplify the final steps in a genome project. Specifically finalizing the locations of contigs and annotations in an assembly. This software also makes it...
Forum: De novo discovery 06-29-2010, 06:53 AM
Replies: 2
Views: 3,770
Posted By michaelbarton
Thank you for answer, it was very helpful in...

Thank you for answer, it was very helpful in understanding our problem. Your jigsaw puzzle analogy makes sense. We consider the option of using 454 with a large insert size.
Forum: De novo discovery 06-28-2010, 11:36 AM
Replies: 2
Views: 3,770
Posted By michaelbarton
How to bridge genome gaps resulting from repeats?

We sequenced a Pseudomonas genome which resulted in several 454 scaffolds. From examining the sequence data it looks like there are many gaps in the sequence because of repeated rRNA genes. Newbler...
Forum: Bioinformatics 06-11-2010, 12:50 PM
Replies: 0
Views: 2,100
Posted By michaelbarton
Question Segmentation fault in consed

I have assembled sequence data from half a 454 plate. The data was assembled with newbler and appears to have gaps due to problems resolving repeats e.g. repeated rRNA genes. I've heard that consed's...
Forum: De novo discovery 01-23-2010, 03:04 PM
Replies: 2
Views: 3,100
Posted By michaelbarton
Thanks for the suggestion, we will try to get...

Thanks for the suggestion, we will try to get paired end reads as hopefully this should improve the assembly.
Forum: 454 Pyrosequencing 01-23-2010, 03:03 PM
Replies: 2
Views: 1,850
Posted By michaelbarton
Question Rubber gasket vs. Molecular Markers

We're just about to do some 454 sequencing and de novo assembly of bacterial genomes. We're considering using molecular markers to sequence multiple different genomes instead of the rubber gasket to...
Forum: De novo discovery 01-19-2010, 09:42 AM
Replies: 2
Views: 3,100
Posted By michaelbarton
Question Getting started with de novo genome sequencing

I'm new to genome sequencing and I'd like to ask for some general advice. We'd like to sequence as many P. fluorescens (Pf) strains as we can manage whilst try to get a reasonable assembly. We're...
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