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.