Category Archives: Misc

Kmer spectrum primer

We’ve prepared a short primer on understanding the kmer spectrum plots produced by ALLPATHS-LG. Such plots can prove invaluable when investigating problems, and we recommend that users look at them as a matter of course.

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Choosing the right hardware

Would you like to help us benchmark servers? We are contemplating server purchases and would like to get the most bang for our buck. We imagine that some of you are in the same situation. Therefore, to share intelligence, we … Continue reading

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Assessing assembly methods

For purposes of assessing our assembly methods, we generated some NA12878 clone reference sequences.  We believe that these data will be of interest to the community and have therefore decided to make them available to all. These clone sequences and the … Continue reading

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A test for your system

We’ve started a testing page, which currently has a single speed test which we have used as a ‘sanity check’ for the health of a machine. This is important, and is the first thing to try if ALLPATHS-LG seems to … Continue reading

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Need Help? Maybe the answer is in our FAQ…

We get many questions from users, but a few keep recurring again and again. We’ve created an FAQ containing answers to these common questions, so perhaps the solution to your particular problem can be already be found here…

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Broad Illumina Boot Camp

People generating data for ALLPATHS-LG may want to check out the Broad/Illumina Genome Analyzer Boot Camp, which has presentation materials designed to help you get the most out of the Ilumina sequencing system.

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What to do about contamination

Suppose that you’re trying to sequence species X, but you’ve got contamination from other species mixed in. What can be done about this? Let’s suppose that the other species are similar to species in Genbank. Then you have two main … Continue reading

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New lab method to reduce bias at high GC

Here it is: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. We strongly recommend that this method be used to make libraries for assembly.

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The two most common inquiries

The two most common questions we’ve gotten are of the following sort: 1. I’m having trouble installing ALLPATHS-LG. These are invariably related to general problems with an individual system’s configuration. Provided that you’re running on a 64-bit Linux system, they … Continue reading

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Put this on our wish list

We think that the ideal way to develop and test genome assembly methodology (both laboratory and computational) is to gather a set of ‘control’ genomes that can be sequenced and assembled over and over as the technologies improve. For this … Continue reading

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