Category Archives: News

DISCOVAR is here!

The ALLPATHS-LG team have been busy lately working on a new project: DISCOVAR is both a genome assembler and a variant caller. It requires only a single Illumina fragment library to run, leading to cheaper genome assemblies and low cost … 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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GCC 4.7.0 or higher now required to build ALLPATHS-LG

As of release 44849, GCC 4.7.0 (or higher) is now required to build ALLPATHS-LG. We have made this transition in order to benefit from the many exciting new features afforded by the C++11 standard. If you are unable to access the latest … Continue reading

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FASTG specification released

The FASTG Format Specification Working Group is pleased to announce version 1.0 of the FASTG specification FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. Currently genome assemblies are represented linearly, … Continue reading

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Transitioning to community support for ALLPATHS-LG

Over the past two years we have provided direct support to ALLPATHS-LG users. We believe this has been valuable to all, including us, as it has allowed us to improve our product — making it easier to install and use, … Continue reading

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Stand alone Error Correction now supports paired reads

The error correction script now supports paired end reads. Simply supply two Fastq files (one for each read direction) and the corrected reads will be returned in the same format. In addition, you may also now run the fragment filling code … Continue reading

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Easy stand alone Error Correction

The ALLPATHS-LG fragment read error correction modules are now available for stand alone use outside the full assembly pipeline. You can now easily error correct your own data using our method without running an assembly. Simply supply a Fastq file … Continue reading

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Bacterial example data now available

Don’t have any suitable data yet, but would still like to try out ALLPATHS-LG? In support of our recent hybrid assembly paper, we have provided data suitable for both Illumina only and Illumina + Pacific Biosciences bacterial assemblies.  For something larger you … Continue reading

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Broad Institute to offer genome sequencing and assembly service for bacterial genomes.

The Broad Institute is preparing to offer a service that takes as input a bacterial DNA sample and provides as output a genome assembly based on the new laboratory and computational methods. For further information please write to AssemblyService@broadinstitute.org.

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ALLPATHS-LG available on Blacklight at PSC

The Pittsburgh Supercomputing Center has installed and tested ALLPATHS-LG on Blacklight, a gigantic shared-memory computer. This could be particularly valuable for small labs that would otherwise not have access to a large-memory machine. We thank Philip Blood at PSC and … Continue reading

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