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Downloads and Upgrades: BioJava 3.1.0, Ensembl Genomes 23, GenBak 203.0, and more


BioJava 3.1.0 is available here and from the maven repository.

This release includes bug fixes and new features including CE-CP version 1.4, with additional parameters; an update to SCOPe 2.04; improvements in FASTQ parsing; and minor fixes in structure alignments.

Release 23 of Ensembl Genomes is available here.

In this release, new genomes have been added to Ensembl bacteria, Ensembl metazoa, Ensemble fungi, Ensembl plants, and Ensembl protists.

Also, the REST server provided by Ensembl Genomes has now been updated to use the latest v3.0.0 codebase provided by Ensembl, plus supplementary endpoints for genome discovery and bacterial family/genome retrieval.

The National Center for Biotechnology Information has released GenBank 203.0 via ftp.

Uncompressed 203.0 flatfiles require roughly 652 gigabytes for sequence files only. The ASN.1 data require approximately 544 gigabytes.

The NCBI has also released Genome Workbench 2.8.0. New features in this version include the ability to export alignments to tab delimited format, and new flexible broadcasting between bio trees.

Finally, NCBI has released a major revision of the genomes ftp site. The new site structure provides a single entry point to access sequence and annotation content of both GenBank and RefSeq genomes data, and it can be accessed directly via ftp, or from links provided in NCBI’s Assembly database.

Additional details are available here and here.

A new portal for information contained in the Encyclopedia of DNA Elements has been released.

The portal contains tools for browsing and searching data generated by the ENCODE consortium via assays, biological samples, and experimental reagents used. It includes all released ENCODE data from the production phase of the project, including newer data for 700+ assays that have been released in June and July of this year under a rapid release policy.

Researchers at the Wellcome Trust Sanger Institute have updated Samtools.

Samtools 1.0 enables researchers to read and write data in the new CRAM format, in addition to the existing SAM and BAM file formats for genomic sequence information.

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