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QDD3 aims to improve primer design in the following ways

The current length of Illumina sequencing (100-250 bp) is still slightly short for microsatellite marker development. However, sequencing of hundreds of Gbases of DNA has become affordable and thus – at least for not too big and repetitive genomes - sequences can be assembled into contigs. QDD3 does NOT do de novo assembly, but can take contigs (scaffolds/chormosomes) as an input, and extracts microsatellites with their flanking regions for primer design.

Although the all-against-all comparison of the sequences in QDD versions 1 and 2 could pinpoint some of the putative interspersed or tandem repetitive regions, now a comparison to known repetitive elements via RepeatMasker is also available for the linux comand line version or in the virtual machine.

In previous versions an automatic selection of the 'best' primer-pair was based arbitrary on the penalty score of the primer pairs calculated by Primer3. However based on our wet lab results, this is not a good indicator of PCR success. The new choice of one primer pair per locus now depends on our wet lab tests, and provides more meaningful selection.

Multi-threading for BLAST and RepeatMasker is possible.

Fastq files can also be used as input file (the default option is the fasta format).

Environment Modules

Run module spider qdd to find out what environment modules are available for this application.

System Variables

  • HPC_QDD_DIR - installation directory
  • HPC_QDD_CFG - sample configuration file directory. Copy the 'set_qdd_default.ini' sample configuration file to your working directory and adjust as needed.
  • HPC_QDD_EXE - sample and reference data directory