One-step genotyping tools for targeted long-read sequencing
Project description
DAJIN2 is a genotyping software designed for organisms that have undergone genome editing, utilizing nanopore sequencing technology.
The name DAJIN is inspired by the term 一網打尽 (Ichimou DAJIN or Yīwǎng Dǎjìn), which signifies capturing everything in a single net.
Disclaimer
DAJIN2 is still in the development phase.
Basic tests covering point mutations, deletions, and insertion designs have been conducted.
If you encounter any bugs or issues, please report them via Issues.
Installation
To install DAJIN2, simply run the following command:
pip install DAJIN2
Usage
Single Sample Analysis
DAJIN2 allows for the analysis of single samples (one sample vs one control).
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 the example dataset
wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-single.tar.gz
tar -xf example-single.tar.gz
# Run DAJIN2
DAJIN2 \
--name stx2-deletion \
--sample example-single/sample.fq.gz \
--control example-single/control.fq.gz \
--allele example-single/design.fa \
--genome mm39 \
--threads 10
# 2023-06-04 11:30:03: example-single/control.fq.gz is now processing...
# 2023-06-04 11:30:06: Preprocess example-single/control.fq.gz...
# 2023-06-04 11:30:06: Mapping example-single/control.fq.gz...
# 2023-06-04 11:30:21: Call MIDSV example-single/control.fq.gz...
# 2023-06-04 11:30:31: 🍵 example-single/control.fq.gz is finished!
# 2023-06-04 11:30:31: example-single/sample.fq.gz is now processing...
# 2023-06-04 11:30:35: Preprocess example-single/sample.fq.gz...
# 2023-06-04 11:34:13: Classify example-single/sample.fq.gz...
# 2023-06-04 11:34:18: Clustering example-single/sample.fq.gz...
# 2023-06-04 11:35:01: Consensus calling example-single/sample.fq.gz...
# 2023-06-04 11:35:08: 🍵 example-single/sample.fq.gz is finished!
# 🎉 Finished! Open DAJINResults/stx2-deletion to see the report.
Batch Processing
DAJIN2 can also 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
# Donwload the example dataset
wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-batch.tar.gz
tar -xf example-batch.tar.gz
# Run DAJIN2
DAJIN2 batch --file example-batch/batch.csv --threads 3
# 2023-07-31 17:01:10: example-batch/tyr_control.fq.gz is now processing...
# 2023-07-31 17:01:16: Preprocess example-batch/tyr_control.fq.gz...
# 2023-07-31 17:01:48: Output BAM files of example-batch/tyr_control.fq.gz...
# 2023-07-31 17:01:52: 🍵 example-batch/tyr_control.fq.gz is finished!
# 2023-07-31 17:01:52: example-batch/tyr_c230gt_50%.fq.gz is now processing...
# 2023-07-31 17:01:52: example-batch/tyr_c230gt_10%.fq.gz is now processing...
# 2023-07-31 17:01:52: example-batch/tyr_c230gt_01%.fq.gz is now processing...
# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:02:17: Classify example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:02:19: Clustering example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:02:34: Classify example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:02:35: Classify example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:02:53: Consensus calling of example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:02:59: Output reports of example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:03:04: 🍵 example-batch/tyr_c230gt_50%.fq.gz is finished!
# 2023-07-31 17:03:39: Consensus calling of example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:03:51: Output reports of example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:04:03: 🍵 example-batch/tyr_c230gt_01%.fq.gz is finished!
# 2023-07-31 17:04:08: Consensus calling of example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:04:16: Output reports of example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:04:24: 🍵 example-batch/tyr_c230gt_10%.fq.gz is finished!
# 🎉 Finished! Open DAJINResults/tyr-substitution to see the report.
References
For more information, please refer to the following publication:
Project details
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.