ITDiscover

Tool for discovering FLT3 ITDs from amplicon sequencing of AML samples

Installation

The recommended way to install ITDiscover is via conda, using the MOMA-AUH channel:

conda install MOMA-AUH::itdiscover

Usage

itdiscover --help
itdiscover --version

Example:

itdiscover \
  --reference reference.fasta \
  --r1 sample_R1.fastq.gz \
  --r2 sample_R2.fastq.gz \
  --forward-primer GGGTTT \
  --reverse-primer AAACCC \
  --output report.html

The --output flag writes an HTML report with one representative alignment per called duplication. Primer trimming is optional and can be enabled with --forward-primer and --reverse-primer.