DAJIN2 0.1.19

One-step genotyping tools for Nanopore amplicon sequencing

DAJIN2 is now under development👷

I aim to release a stable version of DAJIN2 by March 2023:crossed_fingers:

New planned features

Experiments

• support nCATs
• support PacBio
• multi-allele phasing

Functions

• output VCF
• support multi-processing
• trim microhomology in BAM

Usability

• easy installation
  • pypi
  • bioconda
  • docker image
• support low-/middle-spec laptop
• support macOS
• support samples without a reference genome
• support visualization using igv.js via DAJIN2 view command
• support graphical user interface using flask via DAJIN2 gui command

Maintainability

• tests
• minimize dependencies
  • Python, R, Bash -> Python
  • samtools -> pysam
  • minimap2 -> mappy
  • remove NanoSim
  • remove Tensorflow (GPU computation)