Reference Databases

IGGdb High-Quality Gut Genomes

• Pre-computed bowtie2 indexes

• Representative genomes for human gut species with a high-quality genome (N=2,935)

• Citation: Nayfach, S, et al. “New insights from uncultivated genomes of the global human gut microbiome.” Nature 568.7753 (2019): 505-510.

• Download Link (11.2 GB): https://dl.dropboxusercontent.com/s/9fq2vck1dugmic5/IGG_v1.0_split.tar.gz

IGGdb High-Quality Genomes Across Environments

This database is too large to host bowtie2 indexes. However, you can download it directly and index with CoPTR. We recommended breaking the database into several smaller indexes, such that each index contains fewer than 4 billion bases. This allows bowtie2 to create a small index for each subset. You can merge reads mapped to multiple indexes with the merge command.

• Representative genomes for species with a high-quality genome (N=16,136)

• Download link available from https://github.com/snayfach/IGGdb

• Citation: Nayfach, S, et al. “New insights from uncultivated genomes of the global human gut microbiome.” Nature 568.7753 (2019): 505-510.