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This paper is a revised and extended version of reference [Ohkami T, Nagao J, Koyama S. Parameter identification method using wavelet transform.
Based on the latest version of reference human genome sequence (Build 34, July 2003 freeze) the MDRs are covered by two sequence contigs (NT_004321 and NT_004547) with a gap of suggested size of 50 kb between these contigs.
To keep the predicted targets up-to-date, the database will be updated according to the new version of reference genome data once a year, due to the great burden in computational complexity of these predicted targets.
After the data were extracted from The Sequence Read Archive [ 20], we performed the alignment with Bowtie 2 [ 21] allowing 1 mismatch; human genome version hg38 [ 22] was taken as the most recent version of reference at the time when the analysis was conducted.
For instance, adding an input, reference or output file to the process should result in an increment of the version number while an updated version of reference data, such as a new genome assembly, should not, as long as the process is still executable in the same way; the information about the updated reference file would be contained in the analysis metadata (AMD) (see next section).
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(119) In another version of reference-free alignment, a series of arbitrarily selected images are used in turn as references to align all of the other images.
In addition to the STarT-G, several validated German versions of reference standard instruments were included in the study questionnaire.
Failure to fully embrace the issues surrounding versioning of reference sequences can lead to inconsistency of variant descriptions from one generation of patients to the next.
More effort is thus required to translate data in published papers and databases between different versions of reference sequences [ 21, 22].
Strong efforts at UPPNEX are made to keep redundant data to a minimum and keeping central versions of reference genomes and other common files has been a good way to achieve that.
For each Proton run, "Ion TargetSeq" was used as the application type, human reference hg19 (UCSC version of GRCh37 reference assembly) as the reference library and "Ion-TargetSeq-Exome-50 Mb-hg19_revA.bed" as the target regions bed file.
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