Author Archives: jaffe

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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ALLPATHS-LG faster now

Revision 36405 includes a faster version of error correction, that also reduces i/o usage. In combination with a recent speedup of the “fragment filling” module, ALLPATHS-LG is now about 20% faster.

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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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Improved handling of polymorphism

Revision 35887 introduces some changes that improve the performance of ALLPATHS-LG on polymorphic data sets. On a 10 Mb human test region, the N50 contig size is now 81 kb, roughly double what it was before. More changes are in … Continue reading

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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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Contig accuracy twice as good now

Over the last two months, since we wrote the ALLPATHS-LG paper, the accuracy of contigs generated by the algorithm has been substantially improved.  Here’s a table of  results for a test assembly consisting of the mouse chr 1 region, from … Continue reading

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ALLPATHS-LG in “Bioinform” article on GenomeWeb

Bioinform article. One small note…  The article says that the “team next plans to focus on improving the quality of the data used in the assemblies”.  This is ONE focus!  We are also actively engaged in making ALLPATHS-LG work better … Continue reading

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The PNAS article on ALLPATHS-LG has just appeared

http://www.pnas.org/content/early/2010/12/20/1017351108.full.pdf+html

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