Author Archives: AllpathsIain

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 … Continue reading

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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 … Continue reading

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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 … Continue reading

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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 … 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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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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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 … Continue reading

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Star Nosed Mole assembly released

The ALLPATHS-LG assembly of Star Nosed Mole (Condylura cristata) 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 46.2 55.5 AJFV00000000 ConCri1.0 Please read our … Continue reading

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Degu assembly released

The ALLPATHS-LG assembly of Degu (Octodon degus) 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 19.8 12.1 AJSA00000000 OctDeg1.0 Please read our release terms and … Continue reading

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