genome_downloader

Introduction

This package can be used to download commonly used reference genomes and annotations associated with them. Currently hg19, hg19 and hg19 genomes are supported

Downloading a genome

python -m genome_downloader <genome> <destination>

Genome directory structure

Each genome is downloaded into <destination>/<genome> folder (e.g. python -m genome_downloader mm10 genomes will download data into genomes/mm10 folder)

<destination>
└── <genome>
    │   annotation
    │   ├── ChromInfo.txt               - Chromosome sizes
    │   ├── cytoBand.txt                - Cytoband information
    │   ├── <genome>.chrom.sizes        - Chromosome sizes
    │   ├── <genome>.ncbiRefSeq.gtf.gz  - Genome annotations with putative transcripts
    │   ├── <genome>.refGene.gtf.gz     - Curated genome annotations
    │   └── ucsc_repeatmasker.tsv       - Repeatmasker's repeats coordinates
    ├── <genome>.fa                     - Reference genome
    ├── <genome>.fai                    - Reference genome index
    ├── <genome>.*.bt2                  - Bowtie2 index files
    └── <genome>.rev.*.bt2              - Bowtie2 index files