This repository is a fast way of downloading and assembling genomes from the SRA. A tentative estimate of its speed is that it can download and map 200 microbial genomes per 24 hours per 8 cores.
Requirements:
install SRAtoolkit and Snippy:
brew install sratoolkit
brew install brewsci/bio/snippy
Create a file with 1 run per line:
ERR551085
ERR551223
ERR552204
ERR551150
ERR553349
ERR552113
ERR552505
ERR552942
ERR552440
Run the command(needs to be renamed). At the moment it is limited to the first 2 million spots. This needs to be made into a user input
bash bin/xargs_script.sh AMR_TB_GENOMES ./Reference/GCF_000195955.2_ASM19595v2_genomic.fna