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 August 2023:crossed_fingers:
New planned features
Experiments
- Nanopore R9.4
- Nanopore R10.4
- PacBio
- nCATs
- base-editing
Tested Design
- point mutation
- 2-cut knockout
- flox knockin
- 1-cut knockout
- large insertion knockin
- humanized exon knockin
- multi-allele phasing
Functions
- output VCF
- multi-processing
- error correction
- repetitive deletion
- knockin sequence
- trim microhomology in BAM
Usability
- documentation
- 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 (GUI) using
flaskviaDAJIN2 guicommand
Maintainability
- tests
- minimize dependencies
- Python, R, Bash -> Python
- samtools -> pysam
- minimap2 -> mappy
- remove NanoSim
- remove Tensorflow (GPU computation)
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
DAJIN2-0.1.32a0.zip
(51.6 kB
view hashes)
