One-step genotyping tools for Nanopore amplicon sequencing
Project description
# DAJIN2 is now under development👷
I aim to release a stable version of DAJIN2 by March 2023:crossed_fingers: ## New planned features
### Wet experiments
[ ] support nCATs
[ ] support PacBio
### Functions
[ ] output VCF
[ ] multi-allele phasing
[x] trim microhomology in BAM
### Usability
[ ] easy installation - [ ] PyPI - [ ] BioConda - [ ] docker image
[ ] support low-/middle-spec laptop
[x] support macOS
[x] support samples without a reference genome
[x] support visualization using igv.js via DAJIN2 view command
[x] support graphical user interface using flask via DAJIN2 gui command
### Maintainability
[ ] tests
[x] minimize dependencies - [x] Python, R, Bash -> Python - [x] samtools -> pysam - [x] minimap2 -> mappy - [x] remove NanoSim - [x] remove Tensorflow (GPU computation)
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