Metadata-Version: 2.1
Name: DAJIN2
Version: 0.1.19
Summary: One-step genotyping tools for Nanopore amplicon sequencing
Home-page: https://github.com/akikuno/DAJIN2
Author: Akihiro Kuno
Author-email: akuno@md.tsukuba.ac.jp
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# 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
- [x] trim microhomology in BAM

### Usability

- [ ] easy installation
  - [x] 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)

