Monthly Archives: January 2011

The two most common inquiries

Posted on January 27, 2011 by jaffe

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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ALLPATHS-LG adds support for Fastq and Fasta files.

Posted on January 27, 2011 by AllpathsIain

By popular demand, ALLPATHS-LG can now import sequence data in Fastq and Fasta format – in addition to the already supported BAM format. Full details of how to import BAM, Fastq and Fasta files can be found in the updated … Continue reading →

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Put this on our wish list

Posted on January 19, 2011 by jaffe

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

Posted on January 8, 2011 by jaffe

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

Posted on January 7, 2011 by jaffe

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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ALLPATHS-LG featured in “In Sequence” on Genomeweb

Posted on January 4, 2011 by AllpathsIain

In Sequence article.  See also the article on the Broad website.

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