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Short-read sequencing tools.

Main tools

  • SeqPurge - A highly-sensitive adapter trimmer for paired-end short-read data (paper, poster from ECCB 2016 with more recent benchmarks).
  • SampleCorrelation - Calculates the variant overlap and correlation of two VCF/BAM files.
  • SampleGender - Determines sample gender based on a BAM file.
  • PERsim - Paired-end read simulator for Illumina reads.
  • CnvHunter - CNV detection from targeted resequencing data using non-matched control samples.

Environment Modules

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

System Variables

  • HPC_NGSBITS_DIR - installation directory