makura 1.2.0

NCBI Genome downloader

# Makura: NCBI Genome downloader

## Requirements

• rsync (linux command, required for downloading NCBI genomes)

• python 3.8 (or greater)

## Installation

### Rsync ` conda install -c conda-forge rsync # or sudo apt install rsync `

### Python packages

https://pypi.org/project/makura/

install from Pypi

` pip install makura `

install locally ` python setup.py install `

install from docker ` docker pull hunglin59638/makura `

## Usage

Update the assembly summary and taxonomy information while first using. ` makura update ` It’s ok that you don’t run the command, makura will automatically update if the assembly summary is not found.

Download bacteria and fungi genomes with complete assembly level in RefSeq database.

` makura download --group bacteria,fungi --assembly-level complete --assembly-source refseq --out_dir /path/to/dir `

Print the records of genomes with JSON lines format, default is TAB ` makura summary --accession GCF_016700215.2 --as-json-lines `

Download genomes with selected taxids ` makura download --taxid 2209 `

If you have many items to input, input a file contains lines is supported. Example: taxid_list.txt ` 61645 69218 550 `

` makura download --taxid-list taxid_list.txt --out_dir /path/to/dir `

Tips:

Running with multiple downloads in parallel is supported (Default: 4). We set the maximum is 8 to avoid NCBI blocks the downloads. ` makura download --group bacteria,fungi --parallel 4 `

While downloading the genomes, makura can check the MD5 checksum of them. The MD5 values was stored to a file named md5checksums.txt in output directory.

## Developing function Using the RESTful API to get assembly summary 1. run the API server ` docker run --rm -p 5000:5000 hunglin59638/makura:1.1.0 makura api --port 5000 ` 2. get the summary of assembly accessions ` curl http://localhost:5000/summary?accessions=GCA_002287175.1,GCA_000762265.1 ` ## Features in the future - Creating minimap2 and bwa index using downloaded genomes. - Downloading genomes by organism name, biosample, bioproject, etc.