Species-colored Themisto v3 index with 640k bacterial genomes

This is a Themisto v3 [1] index containing the 639,981 high-quality genomes from 661k bacterial genomes dataset of Blackwell et al. [2]. The index contains all distinct 31-mers of the dataset (both strands). There are 71 billion distinct 31-mers in the data (35.5 billion reverse complement pairs). Each k-mer is annotated with the set of species identifiers that contain that 31-mer. The species identifiers are called colors. There are 2340 distinct colors in the dataset, so the color identifiers range from 0 to 2339. To pseudoalign reads.fastq against the index using 16 threads, install Themisto v3, and use the following command: <pre><code class="language-bash">themisto pseudoalign -q reads.fastq -i themisto_640k/index -t 16 --temp-dir .</code></pre> This will output one line of space-separated integers per read in the input. The first integer on a line is the zero-based rank of the read in the fastq file, and the rest of the integers are the identifiers of colors that are compatible with the read. The file color_names.csv lists the species name and the taxid for each color. The pseudoalignment counts <strong>should not be directly used as abundance estimates</strong> because they only describe which reads are <em>compatible</em> with which species, and a single read may be compatible with many. We recommend using mSWEEP to estimate abundances based on the pseudoalignment data: https://github.com/PROBIC/mSWEEP. -- The index was constructed with Themisto v3.0.0 using the following command line parameters: <pre><code class="language-bash">themisto build -i input_file_list.txt --file-colors --reverse-complements -o 640k_bacteria -m 512000 -t 48 -k 31 --temp-dir temp --verbose -d 20</code></pre> The file source_accessions.txt lists the accession numbers of assemblies included in the database. [1] Alanko, J. N., Vuohtoniemi, J., Maklin, T., &amp; Puglisi, S. J. (2023). Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes. bioRxiv, 2023-02. [2] Blackwell, G. A., Hunt, M., Malone, K. M., Lima, L., Horesh, G., Alako, B. T., ... &amp; Iqbal, Z. (2021). Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences. PLoS biology, 19(11), e3001421.