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Pooler

Jul 20, 2023

Optimise DNA sequencing primer-set combinations

Optimise combinations of primers and minimise the formation of dimers in multiplexed PCR.

Primer Pooler can

  • Check through each proposed pool for combinations that are likely to form dimers

  • Automatically move prospective amplicons between proposed pools to reduce dimer formation

  • Automatically search the genome sequence to find which amplicons overlap, and place their corresponding primers in separate pools

  • Optionally keep pool sizes within a specified range

  • Handle thousands of primers without being slow useful for high-throughput sequencing applications

  • Do all of the above with degenerate primers too.

Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data