DAJIN2 0.2.4

One-step genotyping tools for Targeted long-read sequencing

⚠️ DAJIN2 is currently under development ⚠️

Expected to be available the stable version in August 2023 🤞

Installation (alpha-version)

pip install DAJIN2

Usage

Single-mode

DAJIN2 [-h] [-s SAMPLE] [-c CONTROL] [-a ALLELE] [-n NAME] [-g GENOME] [-t THREADS] [-v]

options:
  -h, --help            show this help message and exit
  -s SAMPLE, --sample SAMPLE
                        Full path to a sample FASTQ file
  -c CONTROL, --control CONTROL
                        Full path to a control FASTQ file
  -a ALLELE, --allele ALLELE
                        Full path to a FASTA file
  -n NAME, --name NAME  Output directory name
  -g GENOME, --genome GENOME
                        Reference genome ID (e.g hg38, mm10) [default: '']
  -t THREADS, --threads THREADS
                        Number of threads [default: 1]
  -v, --version         show program's version number and exit

Example

# donwload example dataset
wget https://github.com/akikuno/DAJIN2/raw/main/examples/single.tar.gz
tar -xf single.tar.gz

DAJIN2 \
    --name stx2-deletion \
    --sample "single/barcode25.fq.gz" \
    --control "single/barcode30.fq.gz" \
    --allele "single/design_stx2.fa" \
    --genome mm10 \
    --threads 10

# 2023-06-04 11:30:03: single/barcode30.fq.gz is now processing...
# 2023-06-04 11:30:06: Preprocess single/barcode30.fq.gz...
# 2023-06-04 11:30:06: Mapping single/barcode30.fq.gz...
# 2023-06-04 11:30:21: Call MIDSV single/barcode30.fq.gz...
# 2023-06-04 11:30:31: 🍵 single/barcode30.fq.gz is finished!
# 2023-06-04 11:30:31: single/barcode25.fq.gz is now processing...
# 2023-06-04 11:30:35: Preprocess single/barcode25.fq.gz...
# 2023-06-04 11:34:13: Classify single/barcode25.fq.gz...
# 2023-06-04 11:34:18: Clustering single/barcode25.fq.gz...
# 2023-06-04 11:35:01: Consensus calling single/barcode25.fq.gz...
# 2023-06-04 11:35:08: 🍵 single/barcode25.fq.gz is finished!
# 🎉 Finished! Open DAJINResults/stx2-deletion to see the report.

Batch-mode

DAJIN2 can handle multiple FASTQ files using the `batch' subcommand.

DAJIN2 batch [-h] -f FILE [-t THREADS]

options:
  -h, --help            Show this help message and exit
  -f FILE, --file FILE  CSV or Excel file
  -t THREADS, --threads THREADS
                        Number of threads [default: 1]

Example

🚧 Working in progress 🚧

GUI-mode

You can use DAJIN2 with a graphical user interface (GUI) via the gui subcommand.

DAJIN2 gui

Example

🚧 Working in progress 🚧

References

Kuno A, et al. (2022) DAJIN enables multiplex genotyping to simultaneously validate intended and unintended target genome editing outcomes. PLoS Biology 20(1): e3001507.