genome-downloader 0.0.6

A package to download genome, annotations and bowtie2 indexes

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