American Pika assembly released

The ALLPATHS-LG assembly of the American Pika (Ochotona princeps) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below:

Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP
42.3 26.9 ALIT00000000 OchPri3.0

Please read our release terms and conditions.

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Common Shrew assembly released

The ALLPATHS-LG assembly of the Common Shrew (Sorex araneus) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below:

Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP
22.6 22.8 AALT00000000 SorAra2.0

Please read our release terms and conditions.

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Building fosmid libraries for ALLPATHS-LG

Fosmid libraries provide long range linking information that can vastly improve the size of an assembly’s scaffolds.  Whilst these optional libraries are not required for small genomes, we do recommend them if you are trying to assemble anything large. However, building libraries with insert sizes of ~40 kb can be very difficult.

To this end, the Broad Institute has developed a new method called “Fosill” for creating such libraries. Our manuscript “Paired-end sequencing of Fosmid libraries by Illumina” was recently posted as an accepted preprint in Genome Research. Please direct any questions on the method to the paper’s corresponding author.

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Rhino assembly released

The ALLPATHS-LG assembly of Rhino (Ceratotherium simum simum) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below:

Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP
93.0 26.3 AKZM00000000 CerSimSim1.0

Please read our release terms and conditions.

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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 can try assembling M. zebra,  which was sequenced at the Broad and is now available from the Assemblathon competition website.

Please first try assembling our small example data set before progressing to these larger genomes.

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Jerboa assembly released

The ALLPATHS-LG assembly of Jerboa (Jaculus jaculus) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below:

Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP
15.7 22.1 AKZC00000000 JacJac1.0

Please read our release terms and conditions.

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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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Finished bacterial genomes from shotgun sequence data using ALLPATHS-LG

Our manuscript “Finished bacterial genomes from shotgun sequence data” was just posted as an accepted preprint in Genome Research.  “By applying a new laboratory design and new assembly algorithm to sixteen samples, we demonstrate that assemblies exceeding finished quality can be obtained from whole-genome shotgun data and automated computation.”  Our method is based on assembling a combination of sequence data from Illumina and Pacific Biosciences.  The algorithm is automatically invoked by ALLPATHS-LG when it is supplied with such data, and is already part of the ALLPATHS-LG release.

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Chinchilla assembly released

The ALLPATHS-LG assembly of Chinchilla (Chinchilla lanigera) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below:

Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP
61.1 21.9 AGCD00000000 ChiLan1.0

Please read our release terms and conditions.

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Multi-threading improved

As of revision 42305, ALLPATHS-LG now sets the environment variable MALLOC_PER_THREAD to 1, which causes each thread to do its own memory allocation. This results in a several percent speed-up, and in some cases, a much greater improvement. We anticipate that the change could result in problems on some systems, so if you encounter strange behavior, please let us know.

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