Software packages capable of aligning roughly 9000 bp

[josecolquitt]

I am currently working

[peromhc]

you'll probably need to give a few more details if you expect to get any help.. I this one 9000bp contig, 900 100bp Illumina reads, something else?

To what genome are you trying to align these bases?

[lh3]

bwasw. it works for 100bp-100kbp, against the human genome.

[NGSfan]

I am currently working

While the topic is interesting - I think your forum etiquette is a bit... well let's just say it's unconventional. You'll have to be more specific than that if you want to engage with others and get feedback.

On a side note - it is nice to see there are aligners that can handle longer reads, considering what the future brings!

[josecolquitt]

Problems with Mosaik package

My apologies, I was attempting to delete the entire entry and revise. I am currently working with Simian Immunodeficiency Virus short reads obtained from 454. I am working at an internship trying to gain experience in the bioinformatics field. I am trying to use the Mosaik package in an attempt to sequence these short reads. However, I am having problems with the initialization of this package. Inside the read-me is a tutorial of sorts that guides the user through a demo of the command lists, and then gives a tutorial working with a sample set of C. elegans chromosome 2 reads.

When I attempt to click on any of the programs within the bin directory, a pop up window will display for a fraction of a second and then disappear. I am quite sure that this is simply a result of my inexperience with these programs. Any help or guidance would be greatly appreciated.