Improvements to ALLPATHS-LG hybrid assembly algorithm

Release 41343 includes many changes to the hybrid (Illumina + PacBio) assembly algorithm in ALLPATHS-LG, which result in substantially improved assemblies of bacterial genomes. This completes our work on this problem for now, however we will make changes as needed in response to problems that are reported (if any!).

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Naked Mole Rat assembly released

The ALLPATHS-LG assembly of Naked Mole Rat (Heterocephalus glaber) 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
47.8 20.5 AHKG00000000 nakedmolerat

Please read our release terms and conditions.

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Improved ALLPATHS-LG hybrid assemblies

After months of development, we are excited to announce a major upgrade to ALLPATHS-LG (as of revision 40776). We have switched over to a fundamentally new algorithm for hybrid (short + long read) assembly of small genomes. The algorithm uses the long reads at a much earlier point in the assembly process and is thus able to better exploit the data.  On our test cases, the new algorithm yields dramatically improved results. We are continuing to work on this new method, so expect to see even more improvements over the coming months. Please note that this upgrade only affects hybrid assemblies, and that currently only bacterial sized genomes can be assembled in this manner.
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Manatee assembly released

The ALLPATHS-LG assembly of Manatee (Trichechus manatus latirostris) 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
37.8 14.4 AHIN00000000 TriManLat1.0

Please read our release terms and conditions.

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Spotted Gar assembly released

The ALLPATHS-LG assembly of Spotted Gar (Lepisosteus oculatus) 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
68.6 6.9 AHAT00000000 LepOcu1

Please read our release terms and conditions.

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Male Ferret assembly released

The ALLPATHS-LG assembly of male Ferret (Mustela putorius furo) 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
66.7 9.6 AGTQ00000000 MusPutFurMale1.0

Please read our release terms and conditions.

Details of our female Ferret assembly are given here.

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Guide to using Broad genome assemblies in your research

The ALLPATHS-LG genome assemblies produced here at the Broad Institute are available for download via the Broad FTP site and NCBI. However, some restrictions on their use may apply, and it is therefore important that you follow the guidelines given below.

All of our assemblies are released under the terms of the Fort Lauderdale Agreement, details of which can be found in the Fort Lauderdale Meeting Report and the associated NHGRI Statement. For some background information and a brief discussion on this agreement, please also read the Nature Editorial on the agreement.

If you would like to use any of the Broad ALLPATHS-LG assemblies listed on this blog in your own research, please first contact the Vertebrate Biology Group by emailing them at vertebrategenomes@broadinstitute.org. Please do not email the ALLPATHS-LG team.

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Bye Bye Boost

We try very hard to make sure that ALLPATHS-LG is easy to install and use. Over the last year we have noticed that the dependency on the Boost library was the number one cause of installation problems. So we have re-engineered ALLPATHS-LG to remove all the Boost dependencies from the code, and it now no longer requires the Boost libraries to be installed. We hope this will make life easier for you and your sysadmins.

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Four Cichlid assemblies released

The ALLPATHS-LG assemblies of four Cichlid fish (Pundamilia nyererei, Neolamprologus brichardi, Haplochromis burtoni and Maylandia zebra) are now available via NCBI and the Broad Institute ftp site. The basic statistics and locations are given below:

Species Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP
P. nyererei 22.6 2.5 AFNX00000000 PunNye1.0
N. brichardi 13.0 4.4 AFNY00000000 NeoBri1.0
H. burtoni 21.9 1.2 AFNZ00000000 HapBur1.0
M. zebra 19.9 3.7 AGTA00000000 MetZeb1.1

Please read our release terms and conditions.

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Ground Squirrel assembly released

The ALLPATHS-LG assembly of Ground Squirrel (thirteen-lined) (Spermophilus tridecemlineatus) 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
44.1 8.2 AGTP00000000 groundsquirrel

Please read our release terms and conditions.

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