Author Archives: AllpathsIain

Kmer spectrum primer

We’ve prepared a short primer on understanding the kmer spectrum plots produced by ALLPATHS-LG. Such plots can prove invaluable when investigating problems, and we recommend that users look at them as a matter of course.

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Choosing the right hardware

Would you like to help us benchmark servers? We are contemplating server purchases and would like to get the most bang for our buck. We imagine that some of you are in the same situation. Therefore, to share intelligence, we … Continue reading

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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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Mouse 129 assembly released

The ALLPATHS-LG assembly of Mouse 129 (Mus musculus strain 129Sv/Jae) 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 15.3 6.9 AHBB00000000 mm129svJae1.0 Please read … Continue reading

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Golden Hamster assembly released

The ALLPATHS-LG assembly of Golden Hamster (Mesocricetus auratus) 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 22.5 12.8 APMT00000000 MesAur1.0 Please read our release terms … Continue reading

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Weddell Seal assembly released

The ALLPATHS-LG assembly of Weddell Seal (Leptonychotes weddellii) 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 23.7 0.9 APMU00000000 LepWed1.0 Please read our release terms … 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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Prairie Vole assembly released

The ALLPATHS-LG assembly of Prairie Vole (Microtus ochrogaster) 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 21.2 61.8 AHZW00000000 MicOch1.0 Please read our release terms and … Continue reading

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