iRunner

A simple bacterial genome assembly pipeline for Illumina paired-end reads from NCBI SRA run

Requirements

• Python3.6+
• sra-tools
  • fastq-dump
  • sra-stat
• fastp
• shovill

Quick Start

irunner.py --outdir [path/of/output] --threads [number] [SRA accession]

Usage

arguments:
  accession   NCBI SRA accession
  --outdir    Output folder
  --tmpdir    Directory of temp folder default: '/tmp'
  --gsize     Estimated genome size(MB) eg. 3.2M, If blank will AUTODETECT. default: ''
  --threads   Number of threads to use. default: 8