Lesser Hedgehog Tenrec assembly released

The ALLPATHS-LG assembly of the Lesser Hedgehog Tenrec (Echinops telfairi) 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
20.4 45.8 AAIY00000000 EchTel2.0

Please read our release terms and conditions.

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Big Brown Bat assembly released

The ALLPATHS-LG assembly of Big Brown Bat (Eptesicus fuscus) 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
21.4 13.5 ALEH00000000 EptFus1.0

Please read our release terms and conditions.

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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, and removing bugs that you found. We are grateful for the extensive feedback, comprising of about sixty help tickets a month.

With changes in funding, we are now transitioning to a new support model, based on the community helping itself. To that end we are launching a forum on Google Groups, where users can post questions and hopefully receive answers from their peers. We strongly encourage all users of ALLPATHS-LG to join and actively participate.

If you experience difficulty with ALLPATHS-LG, rather than send a help ticket, please consult our blog, including the FAQ, and if you are still stuck, please consult the forum. We are developing a new assembly algorithm for new data types, and are putting all our efforts into this work. When we release the new algorithm, and pending availability of resources, we may reopen the help system for a period of time.

We thank you for your feedback, and we thank the Broad Institute and our funding agencies NHGRI and NIAID for their support.

The ALLPATHS-LG Team

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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 on your error corrected paired read data. For more details please see the script:

ErrorCorrectReads.pl

Note that you will require a complete and working ALLPATHS-LG installation (r43553+) in order to run this script.

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Cape Elephant Shrew assembly released

The ALLPATHS-LG assembly of the Cape Elephant Shrew (Elephantulus edwardii) 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
24.2 15.0 AMGZ00000000 EleEdw1.0

Please read our release terms and conditions.

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Aardvark assembly released

The ALLPATHS-LG assembly of Aardvark (Orycteropus afer afer) 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
17.7 7.9 ALYB00000000 OryAfe1.0

Please read our release terms and conditions.

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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 and the corrected reads will be returned in the same format. For more details please see the script:

ErrorCorrectReads.pl

Note that you will require a complete and working ALLPATHS-LG installation (r43019+) in order to run this script.

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European Hedgehog assembly released

The ALLPATHS-LG assembly of the European Hedgehog (Erinaceus europaeus) 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
21.4 3.3 AMDU00000000 EriEur2.0

Please read our release terms and conditions.

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Cape Golden Mole assembly released

The ALLPATHS-LG assembly of the Cape Golden Mole (Chrysochloris asiatica) 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
19.6 13.5 AMDV00000000 ChrAsi1.0

Please read our release terms and conditions.

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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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