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NGSPipeDb: NGS Pipelines & Databases

NGSPipeDb is an automated pipeline for parallel processing of huge next generation sequencing (NGS) data and database generation using snakemake workflow which allows for ease of use, optimal speed, and a highly modular code that can be further added onto and customized by experienced users.

Quick start

Required

  • conda
  • pip

Installation

  1. Install from pipi
pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple ngspipedb

Usage example

run RNA-Seq analysis, generate report, and build RNA-Seq database

step1. download test data:

ngspipedb download -n ngspipe-rnaseq-basic -t testdata && tar -zxvf testdata-ngspipe-rnaseq-basic.tar.gz

step2. run rnaseq analysis on test data:

ngspipedb runpipe mouse_rnaseq_analysis -n ngspipe-rnaseq-basic --genomeFasta testdata-ngspipe-rnaseq-basic/genome/chr19.fa --genomeAnno testdata-ngspipe-rnaseq-basic/genome/GRCm38.83.chr19.gtf --samplefile testdata-ngspipe-rnaseq-basic/rawdata/sample.csv --conditionfile testdata-ngspipe-rnaseq-basic/rawdata/condition.csv --rawreadsdir testdata-ngspipe-rnaseq-basic/rawdata -j 10 --report -db

step3. start ngsdb server:

ngspipedb rundb serve -m mouse_rnaseq_analysis/result/ngsdb_code/manage.py -up 127.0.0.1:8000

Tutorial

A more detailed tutorial of how to use this toolkit can be found here:: https://xuanblo.github.io/NGSPipeDb/

Some demos:

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