genomers

genomers is a rust package for downloading genome assembly data and metadata from NCBI

Changelog

• v0.1.5 Added GFF genome annotation to download options

Features

• Download the assembly report and assembly fasta sequence

How to use

The binaries can be downloaded from the 'release' section of the repository (https://github.com/matteobolner/genomers/releases/download/{release}) or with

wget https://github.com/matteobolner/genomers/releases/download/first-release/genomers

Why genomers?

I wanted to have an easy way to download genome assembly data and metadata from NCBI, and since I'm learning rust I decided to try doing it in rust.

How to use

Two parameters are required:
the assembly accession and assembly name.

running "genomers -h" will print all the necessary information.

Example:

# download the assembly report for the E. coli genome

./genomers -a GCA_000005845.2 -n ASM584v2 -r > report.txt

# now the full genome seqeuence

./genomers -a GCA_000005845.2 -n ASM584v2 -g > genome.fasta.gz

The output is directed to stdout and can be piped:

./genomers -a GCA_000005845.2 -n ASM584v2 -r | grep "Chromosome"

# unzip the file
./genomers -a GCA_000005845.2 -n ASM584v2 -g | gunzip > genome.fasta