One-step genotyping tools for Nanopore amplicon sequencing

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  • License: MIT License
  • Author: Akihiro Kuno
  • Requires: Python >=3.7
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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.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)

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for akikuno from gravatar.com akikuno

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: MIT License
  • Author: Akihiro Kuno
  • Requires: Python >=3.7
Classifiers

Release history Release notifications | RSS feed

0.9.1

0.9.0

0.8.0

0.7.4

0.7.3

0.7.2

0.7.1

0.7.0

0.6.2

0.6.1

0.6.0

0.5.6

0.5.5.1

0.5.5

0.5.4

0.5.3

0.5.2

0.5.1

0.5.0

0.4.6

0.4.5

0.4.4

0.4.3

0.4.2

0.4.1

0.4.0

0.3.6

0.3.5

0.3.4

0.3.3

0.3.2

0.3.1

0.3.1b4 pre-release

0.3.0

0.2.4

0.2.3

0.2.2.2

0.2.1

0.2.0

0.1.33

0.1.32a0 pre-release

0.1.30

0.1.22

0.1.21

0.1.20

0.1.19

0.1.18

0.1.17

0.1.16

0.1.15

0.1.14

0.1.13

0.1.12

0.1.11

0.1.10

0.1.9

This version

0.1.8

0.1.7

0.1.6

0.1.5

0.1.4

0.1.3

0.1.2

0.1.1

0.1.0

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