PathoScope is a modular piece of software that will allow you to go all the way from a fastq file to a text file (typically tab-delimited) with columns representing genomes, their proportions, etc.
wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/sralite/ByExp/litesra/DRX/DRX012/DRX012976/DRR014456/DRR014456.sra wget ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra ...
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