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The TRIM database was used to identify the prison location where the health assessment was completed, documentation related to the uptake of STI and BBV testing, and results of testing based on the presence of an appropriate pathology report.
Juvenile females were the least commonly discharged sampling category, and due to the small available sample size, the sample of juvenile females was supplemented with eligible individuals whose records were not available on the TRIM database but were accessible for review at the juvenile remand centre on 9th June 2008.
Prisoner records were sampled using data from the Department of Corrective Services Total Offender Management System TOMSMS) database, which maintains the records of all criminal offenders in Western Australia, and the Total Records and Information Management (TRIM) database, which contains scanned copies of discharged prisoners' paper medical records.
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A trimming database was used to remove reverse transcription adapters (from SMARTer kit) from the sequencing reads prior to assembly.
To trim out poly-A/T, we also included a list of poly-As that contains >10 A in the trimming database.
A UCHIME [ 26] analysis, using the V1-V3 trimmedatabasese as a reference, identified 1.7% of the processed reads from mock samples as likely chimeras.
The sequence of E. coli strain DH10B (NC 010473.1) was used as screening database and the vector pECBAC1 as trimming database, but without 30 bp of sequence flanking either side of the BamHI restriction site (see below) http://hbz7.tamu.edu/homelinks/bac_est/vector/sequence/sequence.htm.htm
The trimming database was developed based on contaminant information obtained from trial assemblies and contains a list of all used adapters and primers with their isoforms identified in the trial assemblies.
To further ensure the quality of the input reads, the contaminant database included in SeqTrim [ 79] package for screening of contaminant sequences such as those of Escherichia coli and cloning vectors was used as the optional trimming database of Newbler, in which a read is screened out if it entirely matches with a sequence in the contaminant database.
The remaining analyses were conducted using the "trimmed" databases for Germany and the Netherlands.
Drizzle aims to be a trim, modular database optimized for cloud computing applications and massive concurrency.
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