# Supporting Data

## Mash: fast genome and metagenome distance estimation using MinHash

RefSeqSketches.msh.gz: Mash sketch database (k=16, s=400) for RefSeq release 70 (48MB)

RefSeqSketchesDefaults.msh.gz: Mash sketch database (k=21, s=1000) for RefSeq release 70 (255MB)

Escherichia.tar.gz: Names and accessions for 500 selected Escherichia genomes, pairwise ANI, and pairwise Jaccard indexes for various k-mer and sketch sizes (24MB)

mash-1.0.tar.gz: Mash version 1.0 codebase (93KB)

SRR2671867.BaAmes.poretools.fastq.gz: Nanopore 1D + 2D sequences generated by poretools (157MB)

SRR2671868.Bc10987.poretools.fastq.gz: Nanopore 1D + 2D sequences generated by poretools (250MB)

## Mash Screen: High-throughput sequence containment estimation for genome discovery

### Custom scripts and intermediate data:

MashScreen_supp.tar.gz

### Data files:

Mash Sketch databases for RefSeq release 88:

  - RefSeq88n.msh.gz: Genomes (k=21, s=1000), 1.2Gb uncompressed

  - RefSeq88p.msh.gz: Proteomes (k=9, s=1000), 1.1Gb uncompressed

art.fastq.gz: Simulated reads for Shakya experiment

Figure 5:

  - fig5.html: Interactive version

  - fig5.tsv: Source data

### Screen of SRA metagenomes vs. RefSeq

> - sra_meta_nucl_95idy.tsv.gz (2.3Gb uncompressed)

> - sra_meta_nucl_80idy_3x.tsv.gz (6.7Gb uncompressed)

> - sra_meta_prot_95idy.tsv.gz (2.1Gb uncompressed)

> - sra_meta_prot_80idy_3x.tsv.gz (8.3Gb uncompressed)

These files have a line for each RefSeq genome listing all metagenomic SRA runs (as of August 2018) with Mash Containment Scores above the specified threshold. They are provided for two screen modes:

- `nucl`: Genomic RefSeq sequences

- `prot`: Proteomic RefSeq sequences (combined amino acid sequences per organism). NOTE: Protein tables above are not p-value filtered and thus large (> ~50Gb) runs may have spurious hits. They also do not contain plasmids. Updates coming soon!

…and at two thresholds:

- `95idy`: 95% Mash Containment Score, any coverage. Useful for finding runs containing a specific genome.

- `80idy_3x`: 80% Mash Containment Score, at least 3x median k-mer multiplicity. Useful for finding related, but novel, sequences.

The files are tab separated, with each line beginning with a RefSeq assembly accession, followed by SRA accessions, for example:

    GCF_000001215.4       SRR3401361      SRR3540373
    GCF_000001405.36      SRR5127794      ERR1539652      SRR413753       ERR206081
    GCF_000001405.38      SRR5127794      ERR1539652      ERR1711677      SRR413753       ERR206081

We also provide simple scripts for searching these files: search.tar

### Public data sources

The BLAST `nr` database was downloaded from `ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*`.

HMP data were downloaded from `ftp://public-ftp.ihmpdcc.org/`, reads from the `Ilumina/` directory and coding sequences from the `HMGI/` directory. Within these folders, sample SRS015937 resides in `tongue_dorsum/` and SRS020263 in `right_retroauricular_crease/`.

SRA runs downloaded with the SRA Toolkit.

RefSeq genomes downloaded from the `genomes/refseq/` directory of `ftp.ncbi.nlm.nih.gov`.

### Public data products

Quebec Polyomavirus is submitted to GenBank as BK010702.