Metagenomes of Swedish lakes. Metagenomes of Swedish lakes

We collected samples from 5 lakes in 2002 and 6 samples from Lake Mälaren in 2021 and 2 Swedish lakes around Uppsala in 2021. We extracted DNA from the samples using 2 different DNA extraction methods and sequenced them using Novaseq 6000. Sequencing reads were quality assessed, followed by assembly and binning. We make the raw reads, assemblies and de replicated bins publicly available through a data article.