DOI: 10.6076/d19p44
title: CONSULT: accurate contamination removal using locality-sensitive hashing

description: A fundamental question appears in many bioinformatics applications: Does a
 sequencing read belong to a large dataset of genomes from some broad
 taxonomic group, even when the closest match in the set is evolutionarily
 divergent from the query? For example, low-coverage genome sequencing
 (skimming) projects either assemble the organelle genome or compute
 genomic distances directly from unassembled reads. Using unassembled reads
 needs contamination detection because samples often include reads from
 unintended groups of species. Similarly, assembling the organelle genome
 needs distinguishing organelle and nuclear reads. While k-mer-based
 methods have shown promise in read-matching, prior studies have shown that
 existing methods are insufficiently sensitive for contamination detection.
 Here, we introduce a new read-matching tool called CONSULT that tests
 whether k-mers from a query fall within a user-specified distance of the
 reference dataset using locality-sensitive hashing. Taking advantage of
 large memory machines available nowadays, CONSULT libraries accommodate
 tens of thousands of microbial species. Our results show that CONSULT has
 higher true-positive and lower false-positive rates of contamination
 detection than leading methods such as Kraken-II and improves distance
 calculation from genome skims. We also demonstrate that CONSULT can
 distinguish organelle reads from nuclear reads, leading to dramatic
 improvements in skim-based mitochondrial assemblies.
description: # Access to the data used for CONSULT benchmarking Date belonging to the
 following paper: * Rachtman, E., Bafna, V., & Mirarab, S. (2021).
 CONSULT: accurate contamination removal using locality-sensitive hashing.
 NAR Genomics and Bioinformatics.
 [doi:10.1093/nargab/lqab071](https://doi.org/10.1093/nargab/lqab071) ##
 Description of the data and file structure ## Drosophila data Genome and
 genome skims used for real Drosophila data analysis are provided. ###
 Before clean-up #### `Dros_fastq_af_bbmerge.tar` This file contains
 deduplicated reads for Drosophila species before clean-up It contains the
 following Drosophila species in fq format: *
 `sub_Drosophila_ananassae_2.fq.gz`: Drosophila ananassae *
 `sub_Drosophila_biarmipes_2.fq.gz`: Drosophila biarmipes *
 `sub_Drosophila_bipectinata_2.fq.gz`: Drosophila bipectinata *
 `sub_Drosophila_erecta_2.fq.gz`: Drosophila erecta *
 `sub_Drosophila_eugracilis_2.fq.gz`: Drosophila eugracilis *
 `sub_Drosophila_mauritiana_2.fq.gz`: Drosophila mauritiana *
 `sub_Drosophila_mojavensis_2.fq.gz`: Drosophila mojavensis *
 `sub_Drosophila_persimilis_2.fq.gz`: Drosophila persimilis *
 `sub_Drosophila_pseudoobscura_2.fq.gz`: Drosophila pseudoobscura *
 `sub_Drosophila_sechellia_2.fq.gz`: Drosophila sechellia *
 `sub_Drosophila_simulans_2.fq.gz`: Drosophila simulans *
 `sub_Drosophila_virilis_2.fq.gz`: Drosophila virilis *
 `sub_Drosophila_willistoni_2.fq.gz`: Drosophila willistoni *
 `sub_Drosophila_yakuba_2.fq.gz`: Drosophila yakuba ####
 `Dros_fastq_af_human_removed.tar` This file contains reads for Drosophila
 species before clean-up but after the removal of human reads. It contains
 the following Drosophila species in fq format: *
 `ucseq_sub_Drosophila_ananassae_2.fq.gz`: Drosophila ananassae *
 `ucseq_sub_Drosophila_biarmipes_2.fq.gz`: Drosophila biarmipes *
 `ucseq_sub_Drosophila_bipectinata_2.fq.gz`: Drosophila bipectinata *
 `ucseq_sub_Drosophila_erecta_2.fq.gz`: Drosophila erecta *
 `ucseq_sub_Drosophila_eugracilis_2.fq.gz`: Drosophila eugracilis *
 `ucseq_sub_Drosophila_mauritiana_2.fq.gz`: Drosophila mauritiana *
 `ucseq_sub_Drosophila_mojavensis_2.fq.gz`: Drosophila mojavensis *
 `ucseq_sub_Drosophila_persimilis_2.fq.gz`: Drosophila persimilis *
 `ucseq_sub_Drosophila_pseudoobscura_2.fq.gz`: Drosophila pseudoobscura *
 `ucseq_sub_Drosophila_sechellia_2.fq.gz`: Drosophila sechellia *
 `ucseq_sub_Drosophila_simulans_2.fq.gz`: Drosophila simulans *
 `ucseq_sub_Drosophila_virilis_2.fq.gz`: Drosophila virilis *
 `ucseq_sub_Drosophila_willistoni_2.fq.gz`: Drosophila willistoni *
 `ucseq_sub_Drosophila_yakuba_2.fq.gz`: Drosophila yakuba ### After
 filtering #### `Dros_fastq_af_consult_filt.tar` This file contains
 Drosophila fastq after filtering with CONSULT. *
 `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila ananassae *
 `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila biarmipes *
 `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila bipectinata *
 `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta *
 `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ####
 `Dros_fastq_af_consult_GTDBfilt_p3c1.tar.gz` This file contains Drosophila
 species filtered with consult against GTDB with settings p = 3, c = 1 *
 `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila ananassae *
 `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila biarmipes *
 `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila bipectinata *
 `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta *
 `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ####
 `Dros_fastq_af_consult_GTDBfilt_p3c2.tar.gz` This file contains Drosophila
 species filtered with consult against GTDB with settings p=3, c = 2 *
 `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila ananassae *
 `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila biarmipes *
 `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila bipectinata *
 `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta *
 `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ####
 `Dros_fastq_af_consult_GTDBfilt_p4c2.tar` This file contains Drosophila
 species filtered with consult against GTDB with settings p = 4, c = 2 *
 `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila ananassae *
 `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila biarmipes *
 `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila bipectinata *
 `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta *
 `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ####
 `Dros_fastq_af_kraken_filt.tar` This file contains Drosophila fastq after
 filtering with Kraken * `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`:
 Drosophila ananassae * `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`:
 Drosophila biarmipes * `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`:
 Drosophila bipectinata * `ucseq_ucseq_sub_Drosophila_erecta_2.fq`:
 Drosophila erecta * `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`:
 Drosophila eugracilis * `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`:
 Drosophila mauritiana * `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`:
 Drosophila mojavensis * `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`:
 Drosophila persimilis * `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`:
 Drosophila pseudoobscura * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`:
 Drosophila sechellia * `ucseq_ucseq_sub_Drosophila_simulans_2.fq`:
 Drosophila simulans * `ucseq_ucseq_sub_Drosophila_virilis_2.fq`:
 Drosophila virilis * `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`:
 Drosophila willistoni * `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`:
 Drosophila yakuba #### `Dros_fastq_af_kraken_GTDBfilt_c0.00.tar` This file
 contains Drosophila reads after filtering with Kraken against GTDB with
 confidence 0.0: * `dimtrx_kraken_gtdbcusTax_Drosfilt_conf0.0.txt`:
 Distance matrix * `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila
 ananassae * `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila
 biarmipes * `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila
 bipectinata * `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta
 * `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ####
 `Dros_fastq_af_kraken_GTDBfilt_c0.04.tar.gz` This file contains Drosophila
 reads after filtering with Kraken against GTDB with confidence 0.4: *
 `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila ananassae *
 `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila biarmipes *
 `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila bipectinata *
 `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta *
 `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ####
 `Dros_fastq_af_kraken_GTDBfilt_c0.05.tar` This file contains Drosophila
 reads after filtering with Kraken against GTDB with confidence 0.05: *
 `ucseq_ucseq_sub_Drosophila_ananassae_2.fq`: Drosophila ananassae *
 `ucseq_ucseq_sub_Drosophila_biarmipes_2.fq`: Drosophila biarmipes *
 `ucseq_ucseq_sub_Drosophila_bipectinata_2.fq`: Drosophila bipectinata *
 `ucseq_ucseq_sub_Drosophila_erecta_2.fq`: Drosophila erecta *
 `ucseq_ucseq_sub_Drosophila_eugracilis_2.fq`: Drosophila eugracilis *
 `ucseq_ucseq_sub_Drosophila_mauritiana_2.fq`: Drosophila mauritiana *
 `ucseq_ucseq_sub_Drosophila_mojavensis_2.fq`: Drosophila mojavensis *
 `ucseq_ucseq_sub_Drosophila_persimilis_2.fq`: Drosophila persimilis *
 `ucseq_ucseq_sub_Drosophila_pseudoobscura_2.fq`: Drosophila pseudoobscura
 * `ucseq_ucseq_sub_Drosophila_sechellia_2.fq`: Drosophila sechellia *
 `ucseq_ucseq_sub_Drosophila_simulans_2.fq`: Drosophila simulans *
 `ucseq_ucseq_sub_Drosophila_virilis_2.fq`: Drosophila virilis *
 `ucseq_ucseq_sub_Drosophila_willistoni_2.fq`: Drosophila willistoni *
 `ucseq_ucseq_sub_Drosophila_yakuba_2.fq`: Drosophila yakuba ### GORG
 Dataset We provide query summary reports (Kraken output) for GORG samples
 searched against TOL, GTDB and Bact/Arch Kraken using Kraken: *
 `gorg_conf0.00_kraken.tar.gz`: conf = 0.00 *
 `gorg_conf0.02_kraken.tar.gz`: conf = 0.02 *
 `gorg_conf0.05_kraken.tar.gz`: conf = 0.05 *
 `gorg_conf0.04_krakenGTDB.tar.gz`: conf = 0.04; note that, as shown in the
 paper, this threshold was only run for the GTDB dataset, which did not
 have enough coverage with other thresholds. Thus, only GTDB is included in
 this directory. We also provide the query sets used during testing: *
 `gorg_all_queries.tar.gz`: Contains the fastq files including the GORG
 query set. Each `.fq` file is one query from GORG. ### Mitochondrial
 Dataset: #### Original sequencing data: * `filt_fastq.tar.gz`: Contains
 filtered reads. Each fastq file is one query. These are after filtering,
 as described in the paper. * `unfiltered_fastq.tar.gz`: Contains
 unfiltered reads ## Chloroplast Data: Original sequencing data: *
 `fastq_affilt.tar.gz`: Contains filtered reads Chloroplast assemblies
 using various assembly methods: * filtered_spades: Spades applied to
 filtered reads * seed: Seed and extend method * base directory: get
 organelle Each nested folder of the following directories includes results
 of getOrganelle (log files, assemblies in fasta format, etc.). **Note:**
 refer to
 [https://github.com/Kinggerm/GetOrganelle](https://github.com/Kinggerm/GetOrganelle) for the description of files included in GetOrganelle results. * `getorganelle_afterfilt.tar.gz`: obtained from filtered reads using getOrganelle * `getorganelle_beforefilt.tar.gz`: obtained from unfiltered reads using getOrganelle Chloroplast annotations: * `annotations.tar.gz`: outputs of annotation software GeSeq; * For each of the eight samples that failed to be assembled fully without filtering (ERR2114804, ERR2114804, SRR2531285, SRR5500897, SRR7685402, SRR2531285, SRR5500897, SRR7685402), we show results of both filtered `filt` and unfiltered `_unfilt` annotations. * `*.fa` files show assemblies, `.gb` shows annotation results, and `.jpg` are drawings of the annotations. ### Bacterial Simulated queries #### `excluded_fna_fq_downSmpl10M.tar` This file contains query samples for TOL query set used in the study * `10x_Cca.fq`: Carya cathayensis * `10x_Cil.fq`: Carya illinoinensis * `10x_Oryza_sativa.fq`: Plant Oryza sativa * `10x_Prunus_persica.fq`: Plant Prunus persica * `15x_Arabidopsis_lyrata.fq`: Plant Arabidopsis lyrata * `20x_Arabidopsis_thaliana.fq`: Plant Arabidopsis thaliana * `250x_Bathycoccus_prasinos.fq`: Plant Bathycoccus prasinos * `2x_Nicotiana_sylvestris.fq`: Plant Nicotiana sylvestris * `2x_Zea_mays.fq`: Plant Zea mays * `5x_Coffee_arabica.fq`: Plant Coffee arabica * `G000007005.fq`: Bacterial/Archaeal species * `G000007185.fq`: Bacterial/Archaeal species * `G000009965.fq`: Bacterial/Archaeal species * `G000011125.fq`: Bacterial/Archaeal species * `G000016385.fq`: Bacterial/Archaeal species * `G000016525.fq`: Bacterial/Archaeal species * `G000017185.fq`: Bacterial/Archaeal species * `G000018365.fq`: Bacterial/Archaeal species * `G000019605.fq`: Bacterial/Archaeal species * `G000022365.fq`: Bacterial/Archaeal species * `G000024305.fq`: Bacterial/Archaeal species * `G000091665.fq`: Bacterial/Archaeal species * `G000145295.fq`: Bacterial/Archaeal species * `G000151105.fq`: Bacterial/Archaeal species * `G000166095.fq`: Bacterial/Archaeal species * `G000173675.fq`: Bacterial/Archaeal species * `G000186365.fq`: Bacterial/Archaeal species * `G000189555.fq`: Bacterial/Archaeal species * `G000190155.fq`: Bacterial/Archaeal species * `G000195935.fq`: Bacterial/Archaeal species * `G000204585.fq`: Bacterial/Archaeal species * `G000215995.fq`: Bacterial/Archaeal species * `G000220645.fq`: Bacterial/Archaeal species * `G000221185.fq`: Bacterial/Archaeal species * `G000223395.fq`: Bacterial/Archaeal species * `G000231015.fq`: Bacterial/Archaeal species * `G000242875.fq`: Bacterial/Archaeal species * `G000243455.fq`: Bacterial/Archaeal species * `G000245135.fq`: Bacterial/Archaeal species * `G000253055.fq`: Bacterial/Archaeal species * `G000264495.fq`: Bacterial/Archaeal species * `G000302455.fq`: Bacterial/Archaeal species * `G000307305.fq`: Bacterial/Archaeal species * `G000317795.fq`: Bacterial/Archaeal species * `G000363885.fq`: Bacterial/Archaeal species * `G000375685.fq`: Bacterial/Archaeal species * `G000389735.fq`: Bacterial/Archaeal species * `G000399765.fq`: Bacterial/Archaeal species * `G000402095.fq`: Bacterial/Archaeal species * `G000421185.fq`: Bacterial/Archaeal species * `G000422285.fq`: Bacterial/Archaeal species * `G000437835.fq`: Bacterial/Archaeal species * `G000446015.fq`: Bacterial/Archaeal species * `G000495715.fq`: Bacterial/Archaeal species * `G000730285.fq`: Bacterial/Archaeal species * `G000746745.fq`: Bacterial/Archaeal species * `G000770635.fq`: Bacterial/Archaeal species * `G000816105.fq`: Bacterial/Archaeal species * `G000830275.fq`: Bacterial/Archaeal species * `G000830295.fq`: Bacterial/Archaeal species * `G000875775.fq`: Bacterial/Archaeal species * `G000955905.fq`: Bacterial/Archaeal species * `G000966265.fq`: Bacterial/Archaeal species * `G001004105.fq`: Bacterial/Archaeal species * `G001189275.fq`: Bacterial/Archaeal species * `G001315825.fq`: Bacterial/Archaeal species * `G001316025.fq`: Bacterial/Archaeal species * `G001316045.fq`: Bacterial/Archaeal species * `G001316145.fq`: Bacterial/Archaeal species * `G001316265.fq`: Bacterial/Archaeal species * `G001317345.fq`: Bacterial/Archaeal species * `G001399695.fq`: Bacterial/Archaeal species * `G001399795.fq`: Bacterial/Archaeal species * `G001402855.fq`: Bacterial/Archaeal species * `G001412615.fq`: Bacterial/Archaeal species * `G001438895.fq`: Bacterial/Archaeal species * `G001481595.fq`: Bacterial/Archaeal species * `G001484685.fq`: Bacterial/Archaeal species * `G001507935.fq`: Bacterial/Archaeal species * `G001508175.fq`: Bacterial/Archaeal species * `G001510225.fq`: Bacterial/Archaeal species * `G001510275.fq`: Bacterial/Archaeal species * `G001510295.fq`: Bacterial/Archaeal species * `G001515215.fq`: Bacterial/Archaeal species * `G001516665.fq`: Bacterial/Archaeal species * `G001516725.fq`: Bacterial/Archaeal species * `G001516745.fq`: Bacterial/Archaeal species * `G001560165.fq`: Bacterial/Archaeal species * `G001560565.fq`: Bacterial/Archaeal species * `G001563335.fq`: Bacterial/Archaeal species * `G001577775.fq`: Bacterial/Archaeal species * `G001587655.fq`: Bacterial/Archaeal species * `G001593925.fq`: Bacterial/Archaeal species * `G001595885.fq`: Bacterial/Archaeal species * `G001627075.fq`: Bacterial/Archaeal species * `G001628455.fq`: Bacterial/Archaeal species * `G001628475.fq`: Bacterial/Archaeal species * `G001674955.fq`: Bacterial/Archaeal species * `G001679155.fq`: Bacterial/Archaeal species * `G001685465.fq`: Bacterial/Archaeal species * `G001717005.fq`: Bacterial/Archaeal species * `G001723845.fq`: Bacterial/Archaeal species * `G001729285.fq`: Bacterial/Archaeal species * `G001776015.fq`: Bacterial/Archaeal species * `G001856825.fq`: Bacterial/Archaeal species * `G001870125.fq`: Bacterial/Archaeal species * `G001887595.fq`: Bacterial/Archaeal species * `G001914405.fq`: Bacterial/Archaeal species * `G001918455.fq`: Bacterial/Archaeal species * `G001918475.fq`: Bacterial/Archaeal species * `G001919175.fq`: Bacterial/Archaeal species * `G001920575.fq`: Bacterial/Archaeal species * `G001940645.fq`: Bacterial/Archaeal species * `G001940655.fq`: Bacterial/Archaeal species * `G001940665.fq`: Bacterial/Archaeal species * `G002009975.fq`: Bacterial/Archaeal species * `G002011035.fq`: Bacterial/Archaeal species * `G002011075.fq`: Bacterial/Archaeal species * `G900109425.fq`: Bacterial/Archaeal species * `G900156635.fq`: Bacterial/Archaeal species ### Reference Libraries Custom Kraken libraries constructed using different genomic reference sets are provided * `kraken_db_gtdb_genomes_reps_r95_k35l31s7_cp.tar.gz`: GTDB datasets with default Kraken taxonomy; this file is too big to be included here and is instead made available on [https://skmer.ucsd.edu/data/consult/kraken/](https://skmer.ucsd.edu/data/consult/kraken/) * `tree_of_life_noViral_unmasked_k35_l31_s7_cp.tar.gz`: TOL with default Kraken taxonomy * `tree_of_life_noViral_unmasked_k35_l31_s7_customtax_cp.tar.gz`: TOL with custom taxonomy ## Sharing/Access information See more on * [CONSULT software repository](https://github.com/noraracht/CONSULT) * [Raw data repository](https://github.com/noraracht/lsh_raw_data) * [Scripts repository](https://github.com/noraracht/lsh_scripts) * [Website with reference files](https://skmer.ucsd.edu/data/consult/)