Java is a programming technology originally developed by Sun Microsystems and later acquired by Oracle. Oracle Java is a proprietary implementation for Java that is free to download and use for commercial use, but not to redistribute, therefore it is not included in a officially maintained repository.
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Oracle does not allow downloads without accepting their license, therefore we needed to modify the header of our request. Alternatively, you can just download the compressed file using your browser and manually upload it using a SFTP/FTP client.
The most significant storage saving in this approach comes from discarding the base qualities after base error correction is carried out. It remains an open question as to what proportion of base qualities need to be retained for accurate variant discovery and genotyping, with increasing evidence showing that discarding or quantile binning of base qualities does not have a detrimental effect (Yu et al. 2015; Ochoa et al. 2016). However, many applications of next-generation sequencing (e.g., clinical sequencing) rely on highly accurate identification of novel rare variants. One alternative approach to completely discarding base qualities could be a controlled loss of base qualities. For example, there could be an iterative process of population BWT construction, where genomes are continually added. Initially, with few genomes, the majority of the sequencing reads will contain novel k-mers, and as more genomes are added, we will observe the same k-mers in multiple individuals across the population. One could envisage an approach where base qualities are only maintained for reads that support novel k-mers, with these k-mers being constantly queried against the BWT for increasing population read support, with the goal of eventually discarding these base qualities as increasing support is observed in the population. One could employ the BEETL-Fastq BWT-based data structure to create a side structure of compressed and searchable indexes of read sequences including base qualities (Janin et al. 2014).
One of the limitations of this approach is that this implementation of a population BWT does not maintain read pair information. In our SNP and indel genotyping, read pair information could be incorporated into the genotyping strategy to derive more accurate genotypes. Read pairs would also be particularly useful for structural variant discovery and genotyping, as most existing structural variation detection algorithms use a combination of split reads and read pairs for supporting evidence (Keane et al. 2014; Layer et al. 2014). In our virus analysis, efficient retrieval of read pairs would enable more rapid localization of the HTLV-1 viral integrations by avoiding the need to realign the full original read set. For SNP and indel discovery, retrieval of read pairs would enable local haplotype assembly and phasing of discovered variants, which could aid correct alignment of highly variable loci into a variation graph (Church et al. 2015), especially with library technologies that conserve long-range phase information (Putnam et al. 2016; Zheng et al. 2016). Recording read pair information could significantly increase the amount of metadata required from just basic sample level information to knowledge of every unique read pair combination or sets of reads from the same molecule. The ability to store and efficiently retrieve all of the read pairs of a sample could enable the use of the population BWT as a highly compressed, searchable, and scalable archival format for sequencing data.
This LiveDVD distribution is highly compressed on the DVD and requires that the system decompresses all the necessary softwares into RAM in order to run. In LiveDVD mode, a minimum of 1024Mb is recommended to use this distribution for simple analysis and hardware compatibility testing. For optimal performance it is however recommended to create a Linux swap partition on one hard disk or even better to install the distribution to hard disk. For professionnal use at least 4Gb of RAM (more is better) is highly recommended for every day work. An hard-disk installation of CAELinux 2013 requires at least a 20Gb ext3/4 partition for "/" and a 4Gb swap partition. At the moment most of the classical chipsets for Intel and AMD platforms are supported with some exceptions especially concerning the latest graphics adapters and some specific laptop devices (some wireless network cards) and very specific hardware like Raid controllers. For more help on hardware support / detection / troubleshooting, you should refer to the great Ubuntu documentation, wikis and forums :
Before writing an image to DVD or USB drive, it is highly recommended that you verify the SHA256 sum (hash) of the ISO file. For instructions, please see HowToSHA256SUM. Below is a list of SHA256 sums to check with your downloaded file.
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