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
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.jsviaDAJIN2 viewcommand - support graphical user interface using
flaskviaDAJIN2 guicommand
Maintainability
- tests
- minimize dependencies
- Python, R, Bash -> Python
- samtools -> pysam
- minimap2 -> mappy
- remove NanoSim
- remove Tensorflow (GPU computation)
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